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4,875 results on '"Vega, Francisco"'

1. Optimizing MIMO Efficiency in 5G through Precoding Matrix Techniques

Author

Díaz-Ruiz, Francisco, Martín-Vega, Francisco J., Gómez, Gerardo, and Aguayo-Torres, Mari Carmen

Subjects
Computer Science - Information Theory, Electrical Engineering and Systems Science - Signal Processing
Abstract

Multiple-Input Multiple-Output (MIMO) systems play a crucial role in fifth-generation (5G) mobile communications, primarily achieved through the utilization of precoding matrix techniques. This paper presents precoding techniques employing codebooks in downlink MIMO-5G wireless communications, aiming to enhance network performance to meet the overarching 5G objectives of increased capacity and reduced latency. We conduct a comparative analysis of various precoding techniques outlined by the 5G standard through diverse simulations across different scenarios. These simulations enable us to assess the performance of the different precoding techniques, ultimately revealing the strengths and weaknesses inherent in Type I and Type II codebooks., Comment: 4 pages, 6 figures

Published
2024

2. Aging-Resistant Wideband Precoding in 5G and Beyond Using 3D Convolutional Neural Networks

Author

Villena-Rodriguez, Alejandro, Martín-Vega, Francisco J., Gómez, Gerardo, Aguayo-Torres, Mari Carmen, and Kaddoum, Georges

Subjects
Computer Science - Information Theory, Electrical Engineering and Systems Science - Signal Processing
Abstract

To meet the ever-increasing demand for higher data rates, 5G and 6G technologies are shifting transceivers to higher carrier frequencies, to support wider bandwidths and more antenna elements. Nevertheless, this solution poses several key challenges: i) increasing the carrier frequency and bandwidth leads to greater channel frequency selectivity in time and frequency domains, and ii) the greater the number of antennas the greater the the pilot overhead for channel estimation and the more prohibitively complex it becomes to determine the optimal precoding matrix. This paper presents two deep-learning frameworks to solve these issues. Firstly, we propose a 3D convolutional neural network (CNN) that is based on image super-resolution and captures the correlations between the transmitting and receiving antennas and the frequency domains to combat frequency selectivity. Secondly, we devise a deep learning-based framework to combat the time selectivity of the channel that treats channel aging as a distortion that can be mitigated through deep learning-based image restoration techniques. Simulation results show that combining both frameworks leads to a significant improvement in performance compared to existing techniques with little increase in complexity., Comment: 13 pages, 9 figures, 3 tables

Published
2024

3. AI-Assisted Dynamic Port and Waveform Switching for Enhancing UL Coverage in 5G NR

Author

Villena-Rodríguez, Alejandro, Gómez, Gerardo, Aguayo-Torres, Mari Carmen, Martín-Vega, Francisco J., Outes-Carnero, José, Ng-Molina, F. Yak, and Ramiro-Moreno, Juan

Subjects
Computer Science - Information Theory
Abstract

The uplink of 5G networks allows selecting the transmit waveform between cyclic prefix orthogonal frequency division multiplexing (CP-OFDM) and discrete Fourier transform spread OFDM (DFT-S-OFDM), which is appealing for cell-edge users using high-frequency bands, since it shows a smaller peak-to-average power ratio, and allows a higher transmit power. Nevertheless, DFT-S-OFDM exhibits a higher block error rate (BLER) which complicates an optimal waveform selection. In this paper, we propose an intelligent waveform-switching mechanism based on deep reinforcement learning (DRL). In this proposal, a learning agent aims at maximizing a function built using available throughput percentiles in real networks. Said percentiles are weighted so as to improve the cell-edge users' service without dramatically reducing the cell average. Aggregated measurements of signal-to-noise ratio (SNR) and timing advance (TA), available in real networks, are used in the procedure. Results show that our proposed scheme greatly outperforms both metrics compared to classical approaches., Comment: 5 pages, 3 figures, 4 tables

Published
2024

4. Direct observation of linear dispersion close to the Fermi level in the topological semimetal WTe$_2$ through Landau quantization at atomic scale

Author

Sánchez-Barquilla, Raquel, Vega, Francisco Martín, Ruiz, Alberto M., Jo, Na Hyun, Herrera, Edwin, Baldoví, José J., Ochi, Masayuki, Arita, Ryotaro, Bud'ko, Sergey L., Canfield, Paul C., Guillamón, Isabel, and Suderow, Hermann

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Condensed Matter - Strongly Correlated Electrons
Abstract

We study the topological Weyl type-II semimetal WTe$_2$ via Scanning Tunneling Microscopy (STM) and Density Functional Theory calculations (DFT). We succesfully determine the band structure at zero field close to the Fermi level by comparing quasiparticle interference (QPI) experiments with DFT. Under magnetic fields, we observe Landau level quantization on atomic scale measurements and find a level sequence evidencing a linearly dispersing portion of the band structure. Our results establish the long sought connection between Weyl cones and Landau quantization in WTe$_2$. Atomic scale Landau quantization emerges as a powerful probe of topological surface states for semimetals, superconductors and topological insulators., Comment: 17 pages, 11 figures

Published
2024

5. MSH6-proficient crypt foci in MSH6 constitutional mismatch repair deficiency: reversion of a frameshifted coding microsatellite to its wild-type sequence

Author

Shia, Jinru, Sanchez-Vega, Francisco, Cho, Stanley, Chen, Jie-Fu, Chen, Chin-Tung, Bhanot, Umesh, Urganci, Nil, Firat, Canan, Ntiamoah, Peter, Isidro, Raymond A., Srivastava, Amitabh, Weiser, Martin R., Mandelker, Diana, Vakiani, Efsevia, Boland, C. Richard, Garcia-Aguilar, Julio, and Stadler, Zsofia K.

Published
2024
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10. Increased expression of CD70 in relapsed acute myeloid leukemia after hypomethylating agents

Author

Marques-Piubelli, Mario L., Kumar, Bijender, Basar, Rafet, Panowski, Siler, Srinivasan, Surabhi, Norwood, Kevin, Prashad, Sacha, Szenes, Victoria, Balakumaran, Arun, Arandhya, Akanksha, Lu, Wei, Khan, Khaja, Duenas, Daniela, McAllen, Salome, Gomez, Javier A, Burks, Jared K., Acharyal, Sunil, Borthakur, Gautam, Wang, Wei-Lien, Wang, Wei, Wang, Sa, Solis, Luisa M., Marin, David, Rezvani, Katayoun, Daher, May, and Vega, Francisco

Published
2024
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11. The status of the human gene catalogue

Author

Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M., Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G., Johnson, Rory, Murphy, Terence D., Pertea, Mihaela, Pruitt, Kim D., Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A., Yandell, Mark, Carninci, Piero, and Salzberg, Steven L.

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods
Abstract

Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the estimated number has shrunk to fewer than 20,000, although the number of distinct protein-coding isoforms has expanded dramatically. The invention of high-throughput RNA sequencing and other technological breakthroughs have led to an explosion in the number of reported non-coding RNA genes, although most of them do not yet have any known function. A combination of recent advances offers a path forward to identifying these functions and towards eventually completing the human gene catalogue. However, much work remains to be done before we have a universal annotation standard that includes all medically significant genes, maintains their relationships with different reference genomes, and describes clinically relevant genetic variants., Comment: 14 pages

Published
2023

12. The SWI/SNF chromatin remodeling subunit DPF2 facilitates NRF2-dependent anti-inflammatory and anti-oxidant gene expression

Author

Mas, Gloria, Man, Na, Nakata, Yuichiro, Martinez-Caja, Concepcion, Karl, Daniel L, Beckedorff, Felipe, Tamiro, Francesco, Chen, Chuan, Duffort, Stephanie, Itonaga, Hidehiro, Mookhtiar, Adnan K, Kunkalla, Kranthi, Valencia, Alfredo M, Collings, Clayton K, Kadoch, Cigall, Vega, Francisco, Kogan, Scott C, Morey, Lluis, Bilbao, Daniel, and Nimer, Stephen D

Subjects
Hematology, Genetics, Cancer, Biotechnology, Regenerative Medicine, Stem Cell Research, Stem Cell Research - Nonembryonic - Non-Human, Vaccine Related, Aetiology, Underpinning research, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Inflammatory and immune system, Mice, Animals, Chromatin, Antioxidants, NF-E2-Related Factor 2, Neoplasms, Chromatin Assembly and Disassembly, Inflammation, Gene Expression, DNA-Binding Proteins, Transcription Factors, Epigenetics, Hematopoietic stem cells, Macrophages, Medical and Health Sciences, Immunology
Abstract

During emergency hematopoiesis, hematopoietic stem cells (HSCs) rapidly proliferate to produce myeloid and lymphoid effector cells, a response that is critical against infection or tissue injury. If unresolved, this process leads to sustained inflammation, which can cause life-threatening diseases and cancer. Here, we identify a role of double PHD fingers 2 (DPF2) in modulating inflammation. DPF2 is a defining subunit of the hematopoiesis-specific BAF (SWI/SNF) chromatin-remodeling complex, and it is mutated in multiple cancers and neurological disorders. We uncovered that hematopoiesis-specific Dpf2-KO mice developed leukopenia, severe anemia, and lethal systemic inflammation characterized by histiocytic and fibrotic tissue infiltration resembling a clinical hyperinflammatory state. Dpf2 loss impaired the polarization of macrophages responsible for tissue repair, induced the unrestrained activation of Th cells, and generated an emergency-like state of HSC hyperproliferation and myeloid cell-biased differentiation. Mechanistically, Dpf2 deficiency resulted in the loss of the BAF catalytic subunit BRG1 from nuclear factor erythroid 2-like 2-controlled (NRF2-controlled) enhancers, impairing the antioxidant and antiinflammatory transcriptional response needed to modulate inflammation. Finally, pharmacological reactivation of NRF2 suppressed the inflammation-mediated phenotypes and lethality of Dpf2Δ/Δ mice. Our work establishes an essential role of the DPF2-BAF complex in licensing NRF2-dependent gene expression in HSCs and immune effector cells to prevent chronic inflammation.

Published
2023

15. Implementation of Parallel Evolutionary Convolutional Neural Network for Classification in Human Activity and Image Recognition

Author

Villegas-Cortez, Juan, Román-Alonso, Graciela, Fernandez De Vega, Francisco, Flores-Morales, Yafte Aaron, Cordero-Sanchez, Salomon, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Calvo, Hiram, editor, Martínez-Villaseñor, Lourdes, editor, and Ponce, Hiram, editor

Published
2024
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16. Superconducting density of states and bandstructure at the surface of the candidate topological superconductor Au2Pb

Author

Martín-Vega, Francisco, Herrera, Edwin, Wu, Beilun, Barrena, Víctor, Mompeán, Federico, García-Hernández, Mar, Canfield, Paul C., Black-Schaffer, Annica M., Baldoví, José J., Guillamón, Isabel, and Suderow, Hermann

Subjects
Condensed Matter - Superconductivity, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

The electronic bandstructure of Au$_2$Pb has a Dirac cone which gaps when undergoing a structural transition into a low temperature superconducting phase. This suggests that the superconducting phase ($T_c=1.1$ K) might hold topological properties at the surface. Here we make Scanning Tunneling Microscopy experiments on the surface of superconducting Au$_2$Pb. We measure the superconducting gap and find a sizeable superconducting density of states at the Fermi level. We discuss possible origins for this finding in terms of superconductivity induced into surface states.

Published
2022
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19. Simplified feedback control system for Scanning Tunneling Microscopy

Author

Martín-Vega, Francisco, Barrena, Víctor, Sánchez-Barquilla, Raquel, Fernández-Lomana, Marta, Llorens, José Benito, Wu, Beilun, Fente, Antón, Duplain, David Perconte, Horcas, Ignacio, López, Raquel, Blanco, Javier, Higuera, Juan Antonio, Mañas-Valero, Samuel, Jo, Na Hyun, Schmidt, Juan, Canfield, Paul C., Rubio-Bollinger, Gabino, Rodrigo, José Gabriel, Herrera, Edwin, Guillamón, Isabel, and Suderow, Hermann

Subjects
Condensed Matter - Other Condensed Matter, Physics - Instrumentation and Detectors
Abstract

A Scanning Tunneling Microscope (STM) is one of the most important scanning probe tools available to study and manipulate matter at the nanoscale. In a STM, a tip is scanned on top of a surface with a separation of a few \AA. Often, the tunneling current between tip and sample is maintained constant by modifying the distance between the tip apex and the surface through a feedback mechanism acting on a piezoelectric transducer. This produces very detailed images of the electronic properties of the surface. The feedback mechanism is nearly always made using a digital processing circuit separate from the user computer. Here we discuss another approach, using a computer and data acquisition through the USB port. We find that it allows succesful ultra low noise studies of surfaces at cryogenic temperatures. We show results on different compounds, a type II Weyl semimetal (WTe$_2$), a quasi two-dimensional dichalcogenide superconductor (2H-NbSe$_2$), a magnetic Weyl semimetal (Co$_3$Sn$_2$S$_2$) and an iron pnictide superconductor (FeSe)., Comment: Instrumentation paper

Published
2022
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20. Joint Distribution of Distance and Angles in Finite Wireless Networks

Author

Martín-Vega, Francisco J., Gómez, Gerardo, Morales-Jiménez, David, López-Martínez, F. Javier, and Aguayo-Torres, Mari Carmen

Subjects
Computer Science - Information Theory, Electrical Engineering and Systems Science - Signal Processing
Abstract

Directional beamforming will play a paramount role in 5G and beyond networks in order to combat the higher path losses incurred at millimeter wave bands. Appropriate modeling and analysis of the angles and distances between transmitters and receivers in these networks are thus essential to understand performance and limiting factors. Most existing literature considers either infinite and uniform networks, where nodes are drawn according to a Poisson point process, or finite networks with the reference receiver placed at the origin of a disk. Under either of these assumptions, the distance and azimuth angle between transmitter and receiver are independent, and the angle follows a uniform distribution between $0$ and $2\pi$. Here, we consider a more realistic case of finite networks where the reference node is placed at any arbitrary location. We obtain the joint distribution between the distance and azimuth angle and demonstrate that these random variables do exhibit certain correlation, which depends on the shape of the region and the location of the reference node. To conduct the analysis, we present a general mathematical framework which is specialized to exemplify the case of a rectangular region. We then also derive the statistics for the 3D case where, considering antenna heights, the joint distribution of distance, azimuth and zenith angles is obtained. Finally, we describe some immediate applications of the present work, including the analysis of directional beamforming, the design of analog codebooks and wireless routing algorithms., Comment: 16 pages, 10 figures

Published
2022

22. Correction: “The 5th edition of The World Health Organization Classification of Haematolymphoid Tumours: Lymphoid Neoplasms” Leukemia. 2022 Jul;36(7):1720–1748

Author

Alaggio, Rita, Amador, Catalina, Anagnostopoulos, Ioannis, Attygalle, Ayoma D., de Oliveira Araujo, Iguaracyra Barreto, Berti, Emilio, Bhagat, Govind, Borges, Anita Maria, Boyer, Daniel, Calaminici, Mariarita, Chadburn, Amy, Chan, John K. C., Cheuk, Wah, Chng, Wee-Joo, Choi, John K., Chuang, Shih-Sung, Coupland, Sarah E., Czader, Magdalena, Dave, Sandeep S., de Jong, Daphne, Di Napoli, Arianna, Du, Ming-Qing, Elenitoba-Johnson, Kojo S., Ferry, Judith, Geyer, Julia, Gratzinger, Dita, Guitart, Joan, Gujral, Sumeet, Harris, Marian, Harrison, Christine J., Hartmann, Sylvia, Hochhaus, Andreas, Jansen, Patty M., Karube, Kennosuke, Kempf, Werner, Khoury, Joseph, Kimura, Hiroshi, Klapper, Wolfram, Kovach, Alexandra E., Kumar, Shaji, Lazar, Alexander J., Lazzi, Stefano, Leoncini, Lorenzo, Leung, Nelson, Leventaki, Vasiliki, Li, Xiao-Qiu, Lim, Megan S., Liu, Wei-Ping, Louissaint, Jr, Abner, Marcogliese, Andrea, Medeiros, L. Jeffrey, Michal, Michael, Miranda, Roberto N., Mitteldorf, Christina, Montes-Moreno, Santiago, Morice, William, Nardi, Valentina, Naresh, Kikkeri N., Natkunam, Yasodha, Ng, Siok-Bian, Oschlies, Ilske, Ott, German, Parrens, Marie, Pulitzer, Melissa, Rajkumar, S. Vincent, Rawstron, Andrew C., Rech, Karen, Rosenwald, Andreas, Said, Jonathan, Sarkozy, Clémentine, Sayed, Shahin, Saygin, Caner, Schuh, Anna, Sewell, William, Siebert, Reiner, Sohani, Aliyah R., Suzuki, Ritsuro, Tooze, Reuben, Traverse-Glehen, Alexandra, Vega, Francisco, Vergier, Beatrice, Wechalekar, Ashutosh D., Wood, Brent, Xerri, Luc, and Xiao, Wenbin

Published
2023
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23. The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Lymphoid Neoplasms

Author

Alaggio, Rita, Amador, Catalina, Anagnostopoulos, Ioannis, Attygalle, Ayoma D, Araujo, Iguaracyra Barreto de Oliveira, Berti, Emilio, Bhagat, Govind, Borges, Anita Maria, Boyer, Daniel, Calaminici, Mariarita, Chadburn, Amy, Chan, John KC, Cheuk, Wah, Chng, Wee-Joo, Choi, John K, Chuang, Shih-Sung, Coupland, Sarah E, Czader, Magdalena, Dave, Sandeep S, de Jong, Daphne, Du, Ming-Qing, Elenitoba-Johnson, Kojo S, Ferry, Judith, Geyer, Julia, Gratzinger, Dita, Guitart, Joan, Gujral, Sumeet, Harris, Marian, Harrison, Christine J, Hartmann, Sylvia, Hochhaus, Andreas, Jansen, Patty M, Karube, Kennosuke, Kempf, Werner, Khoury, Joseph, Kimura, Hiroshi, Klapper, Wolfram, Kovach, Alexandra E, Kumar, Shaji, Lazar, Alexander J, Lazzi, Stefano, Leoncini, Lorenzo, Leung, Nelson, Leventaki, Vasiliki, Li, Xiao-Qiu, Lim, Megan S, Liu, Wei-Ping, Louissaint, Abner, Marcogliese, Andrea, Medeiros, L Jeffrey, Michal, Michael, Miranda, Roberto N, Mitteldorf, Christina, Montes-Moreno, Santiago, Morice, William, Nardi, Valentina, Naresh, Kikkeri N, Natkunam, Yasodha, Ng, Siok-Bian, Oschlies, Ilske, Ott, German, Parrens, Marie, Pulitzer, Melissa, Rajkumar, S Vincent, Rawstron, Andrew C, Rech, Karen, Rosenwald, Andreas, Said, Jonathan, Sarkozy, Clémentine, Sayed, Shahin, Saygin, Caner, Schuh, Anna, Sewell, William, Siebert, Reiner, Sohani, Aliyah R, Tooze, Reuben, Traverse-Glehen, Alexandra, Vega, Francisco, Vergier, Beatrice, Wechalekar, Ashutosh D, Wood, Brent, Xerri, Luc, and Xiao, Wenbin

Subjects
Cancer, Hematologic Neoplasms, Humans, Lymphoma, World Health Organization, Clinical Sciences, Oncology and Carcinogenesis, Immunology
Abstract

We herein present an overview of the upcoming 5th edition of the World Health Organization Classification of Haematolymphoid Tumours focussing on lymphoid neoplasms. Myeloid and histiocytic neoplasms will be presented in a separate accompanying article. Besides listing the entities of the classification, we highlight and explain changes from the revised 4th edition. These include reorganization of entities by a hierarchical system as is adopted throughout the 5th edition of the WHO classification of tumours of all organ systems, modification of nomenclature for some entities, revision of diagnostic criteria or subtypes, deletion of certain entities, and introduction of new entities, as well as inclusion of tumour-like lesions, mesenchymal lesions specific to lymph node and spleen, and germline predisposition syndromes associated with the lymphoid neoplasms.

Published
2022

24. Millikelvin scanning tunneling microscope at 20/22 T with a graphite enabled stick-slip approach and an energy resolution below 8$\mu$eV: Application to conductance quantization at 20 T in single atom point contacts of Al and Au

Author

Lomana, Marta Fernández, Wu, Beilun, Martín-Vega, Francisco, Barquilla, Raquel Sánchez, Montoya, Rafael Álvarez, Castilla, José María, Navarrete, José, Marijuan, Juan Ramón, Herrera, Edwin, Suderow, Hermann, and Guillamón, Isabel

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Instrumentation and Detectors
Abstract

We describe a scanning tunneling microscope (STM) that operates at magnetic fields up to 22 Tesla and temperatures down to 80 mK. We discuss the design of the STM head, with an improved coarse approach, the vibration isolation system, and efforts to improve the energy resolution using compact filters for multiple lines. We measure the superconducting gap and Josephson effect in Aluminum and show that we can resolve features in the density of states as small as 8\,$\mu$eV. We measure the quantization of conductance in atomic size contacts and make atomic resolution and density of states images in the layered material 2H-NbSe$_2$. The latter experiments are performed by continuously operating the STM at magnetic fields of 20 T in periods of several days without interruption., Comment: 16 pages, 12 figures

Published
2021
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26. Upper Cretaceous Crustacea from Central Cuba

Author

Vega, Francisco J., Nyborg, Torrey, Garassino, Alessandro, Pasini, Giovanni, Aguilar-Pérez, Javier, Borges-Sellén, Carlos R., Arano-Ruiz, Alberto F., Quintero-Vázquez, Servilio J., and Gutiérrez-Domech, Roberto Manuel

Published
2024
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28. A new orientation for the air power doctrine: Spain

Author

Vega, Francisco Jose Garcia de la

Subjects
ROLES AND MISSIONS - Air Force - Spain, AEROSPACE POWER - Spain, DOCTRINE - Air Force - Spain, AIR FORCE - Spain - Equipment
Abstract

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Published
2007

29. An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing

Author

Ramos-Mandujano, Gerardo, Grünberg, Raik, Zhang, Yingzi, Bi, Chongwei, Guzmán-Vega, Francisco J., Shuaib, Muhammad, Gorchakov, Rodion V., Xu, Jinna, Tehseen, Muhammad, Takahashi, Masateru, Takahashi, Etsuko, Dada, Ashraf, Ahmad, Adeel Nazir, Hamdan, Samir M., Pain, Arnab, Arold, Stefan T., and Li, Mo

Published
2023
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31. Molecular profiling of a real-world breast cancer cohort with genetically inferred ancestries reveals actionable tumor biology differences between European ancestry and African ancestry patient populations

Author

Miyashita, Minoru, Bell, Joshua S. K., Wenric, Stephane, Karaesmen, Ezgi, Rhead, Brooke, Kase, Matthew, Kaneva, Kristiyana, De La Vega, Francisco M., Zheng, Yonglan, Yoshimatsu, Toshio F., Khramtsova, Galina, Liu, Fang, Zhao, Fangyuan, Howard, Frederick M., Nanda, Rita, Beaubier, Nike, White, Kevin P., Huo, Dezheng, and Olopade, Olufunmilayo I.

Published
2023
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35. SMARCA4 is a haploinsufficient B cell lymphoma tumor suppressor that fine-tunes centrocyte cell fate decisions

Author

Deng, Qing, Lakra, Priya, Gou, Panhong, Yang, Haopeng, Meydan, Cem, Teater, Matthew, Chin, Christopher, Zhang, Wenchao, Dinh, Tommy, Hussein, Usama, Li, Xubin, Rojas, Estela, Liu, Weiguang, Reville, Patrick K., Kizhakeyil, Atish, Barisic, Darko, Parsons, Sydney, Wilson, Ashley, Henderson, Jared, Scull, Brooks, Gurumurthy, Channabasavaiah, Vega, Francisco, Chadburn, Amy, Cuglievan, Branko, El-Mallawany, Nader Kim, Allen, Carl, Mason, Christopher, Melnick, Ari, and Green, Michael R.

Published
2024
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40. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases

Author

Owen, Mallory J, Lefebvre, Sebastien, Hansen, Christian, Kunard, Chris M, Dimmock, David P, Smith, Laurie D, Scharer, Gunter, Mardach, Rebecca, Willis, Mary J, Feigenbaum, Annette, Niemi, Anna-Kaisa, Ding, Yan, Van Der Kraan, Luca, Ellsworth, Katarzyna, Guidugli, Lucia, Lajoie, Bryan R, McPhail, Timothy K, Mehtalia, Shyamal S, Chau, Kevin K, Kwon, Yong H, Zhu, Zhanyang, Batalov, Sergey, Chowdhury, Shimul, Rego, Seema, Perry, James, Speziale, Mark, Nespeca, Mark, Wright, Meredith S, Reese, Martin G, De La Vega, Francisco M, Azure, Joe, Frise, Erwin, Rigby, Charlene Son, White, Sandy, Hobbs, Charlotte A, Gilmer, Sheldon, Knight, Gail, Oriol, Albert, Lenberg, Jerica, Nahas, Shareef A, Perofsky, Kate, Kim, Kyu, Carroll, Jeanne, Coufal, Nicole G, Sanford, Erica, Wigby, Kristen, Weir, Jacqueline, Thomson, Vicki S, Fraser, Louise, Lazare, Seka S, Shin, Yoon H, Grunenwald, Haiying, Lee, Richard, Jones, David, Tran, Duke, Gross, Andrew, Daigle, Patrick, Case, Anne, Lue, Marisa, Richardson, James A, Reynders, John, Defay, Thomas, Hall, Kevin P, Veeraraghavan, Narayanan, and Kingsmore, Stephen F

Subjects
Human Genome, Pediatric, Genetics, Biotechnology, Pediatric Research Initiative, Good Health and Well Being, Child, DNA Copy Number Variations, Humans, Infant, Retrospective Studies, Whole Genome Sequencing
Abstract

While many genetic diseases have effective treatments, they frequently progress rapidly to severe morbidity or mortality if those treatments are not implemented immediately. Since front-line physicians frequently lack familiarity with these diseases, timely molecular diagnosis may not improve outcomes. Herein we describe Genome-to-Treatment, an automated, virtual system for genetic disease diagnosis and acute management guidance. Diagnosis is achieved in 13.5 h by expedited whole genome sequencing, with superior analytic performance for structural and copy number variants. An expert panel adjudicated the indications, contraindications, efficacy, and evidence-of-efficacy of 9911 drug, device, dietary, and surgical interventions for 563 severe, childhood, genetic diseases. The 421 (75%) diseases and 1527 (15%) effective interventions retained are integrated with 13 genetic disease information resources and appended to diagnostic reports ( https://gtrx.radygenomiclab.com ). This system provided correct diagnoses in four retrospectively and two prospectively tested infants. The Genome-to-Treatment system facilitates optimal outcomes in children with rapidly progressive genetic diseases.

Published
2022

43. Evolutionary characterization of lung adenocarcinoma morphology in TRACERx

Author

Karasaki, Takahiro, Moore, David A., Veeriah, Selvaraju, Naceur-Lombardelli, Cristina, Toncheva, Antonia, Magno, Neil, Ward, Sophia, Bakir, Maise Al, Watkins, Thomas B. K., Grigoriadis, Kristiana, Huebner, Ariana, Hill, Mark S., Frankell, Alexander M., Abbosh, Christopher, Puttick, Clare, Zhai, Haoran, Gimeno-Valiente, Francisco, Saghafinia, Sadegh, Kanu, Nnennaya, Dietzen, Michelle, Pich, Oriol, Lim, Emilia L., Martínez-Ruiz, Carlos, Black, James R. M., Biswas, Dhruva, Campbell, Brittany B., Lee, Claudia, Colliver, Emma, Enfield, Katey S. S., Hessey, Sonya, Hiley, Crispin T., Zaccaria, Simone, Litchfield, Kevin, Birkbak, Nicolai J., Cadieux, Elizabeth Larose, Demeulemeester, Jonas, Van Loo, Peter, Adusumilli, Prasad S., Tan, Kay See, Cheema, Waseem, Sanchez-Vega, Francisco, Jones, David R., Rekhtman, Natasha, Travis, William D., Hackshaw, Allan, Marafioti, Teresa, Salgado, Roberto, Le Quesne, John, Nicholson, Andrew G., McGranahan, Nicholas, Swanton, Charles, and Jamal-Hanjani, Mariam

Published
2023
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44. It is Time for New Perspectives on How to Fight Bloat in GP

Author

de Vega, Francisco Fernández, Olague, Gustavo, Chávez, Francisco, Lanza, Daniel, Banzhaf, Wolfgang, and Goodman, Erik

Subjects
Computer Science - Neural and Evolutionary Computing, Computer Science - Artificial Intelligence, Computer Science - Symbolic Computation
Abstract

The present and future of evolutionary algorithms depends on the proper use of modern parallel and distributed computing infrastructures. Although still sequential approaches dominate the landscape, available multi-core, many-core and distributed systems will make users and researchers to more frequently deploy parallel version of the algorithms. In such a scenario, new possibilities arise regarding the time saved when parallel evaluation of individuals are performed. And this time saving is particularly relevant in Genetic Programming. This paper studies how evaluation time influences not only time to solution in parallel/distributed systems, but may also affect size evolution of individuals in the population, and eventually will reduce the bloat phenomenon GP features. This paper considers time and space as two sides of a single coin when devising a more natural method for fighting bloat. This new perspective allows us to understand that new methods for bloat control can be derived, and the first of such a method is described and tested. Experimental data confirms the strength of the approach: using computing time as a measure of individuals' complexity allows to control the growth in size of genetic programming individuals.

Published
2020
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45. Impact of cumulative dose of brentuximab vedotin on outcomes of frontline therapy for advanced-stage Hodgkin lymphoma

Author

Steiner, Raphael E., Hwang, Steven R., Khurana, Arushi, Habermann, Thomas M., Epperla, Narendranath, Annunzio, Kaitlin, Allen, Pamela Blair, Baird, Katelin, Paulino, Darina, Alderuccio, Juan Pablo, Lossos, Izidore S., David, Kevin, Evens, Andrew M., Pandya, Karan, Bair, Steven M., Kamdar, Manali, Ba Aqeel, Sheeba, Torka, Pallawi, Lynch, Ryan, Smith, Stephen, Feng, Lei, Noorani, Mansoor, Ahmed, Sairah, Nair, Ranjit, Vega, Francisco, Wu, Susan, Fang, Penny, Pinnix, Chelsea C., Gunther, Jillian R., Dabaja, Bouthaina S., and Lee, Hun J.

Published
2023
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49. The Baf Subunit Dpf2 Regulates Resolution of Inflammation By Controlling Macrophage Differentiation Transcription Factor Networks

Author

Mas Martin, Gloria, Man, Na, Karl, Daniel, Martinez, Concepcion, Duffort, Stephanie, Itonaga, Hidehiro, Mookhtiar, Adnan K, Bilbao, Daniel, Kunkalla, Kranthi, Valencia, Alfredo M, Collings, Clayton, Kadoch, Cigall, Vega, Francisco, Kogan, Scott C, and Nimer, Stephen

Subjects
Rare Diseases, Stem Cell Research, Stem Cell Research - Nonembryonic - Non-Human, Hematology, Genetics, Cancer, Biotechnology, Regenerative Medicine, Aetiology, 2.1 Biological and endogenous factors, Underpinning research, 1.1 Normal biological development and functioning, Inflammatory and immune system, Cardiorespiratory Medicine and Haematology, Clinical Sciences, Paediatrics and Reproductive Medicine, Immunology
Abstract

To mount an effective immune response against infectious pathogens or tissue injury, hematopoietic stem cells (HSCs) increase their proliferation and production of myeloid cells, including macrophages, which destroy the pathogens and repair the damaged tissue. Proper resolution of inflammation is essential to restore hematopoietic homeostasis, as unrestrained inflammation can result in life-threatening pathologies such as sepsis, autoimmune disorders and cancer. The molecular mechanisms that control the resolution of inflammation, and how these contribute to disease phenotypes, are poorly understood. BAF (SWI/SNF) complexes are ATPase dependent chromatin-remodeling complexes that play fundamental roles in transcription. BAF complexes use the energy of ATP to modulate the accessibility of transcription factors to DNA and thus, orchestrate the gene expression programs that control proliferation and cellular identity. Genes encoding for BAF subunits are frequently mutated in cancer and developmental disorders. In hematopoietic malignancies, loss-of-function mutations and low expression of specific BAF subunits have been reported in patients with anemia and bone marrow failure. Work from our lab previously demonstrated that the hematopoietic-specific BAF complex subunit Dpf2 cooperates with the transcription factor Runx1 to regulate myeloid differentiation. Based on these studies, we generated a hematopoietic-specific Dpf2 knock-out mouse model and found that mice lacking Dpf2 develop pancytopenia, anemia and an uncontrolled inflammatory response that results in early death. Dpf2-/- peripheral blood samples showed dysplastic features including increased number of polychromatophilic blood cells and Howell-Jolly bodies in erythrocytes. Histopathological analyses revealed the presence of fibrosis and prominent infiltration of histiocytes in multiple organs, including lungs, liver and spleen. Detailed chemical profiling of plasma showed increased levels of multiple pro-inflammatory cytokines, indicative of systemic inflammation. Flow cytometry analyses and Mass cytometry profiling further revealed an expansion of myeloid lineages, specifically monocytes and macrophages, concomitant with severe defects in lymphoid and erythroid differentiation. We also found that Dpf2-/-HSCs had increased serial re-plating capacity and a marked myeloid differentiation bias. To identify the transcription factor networks underlying these phenotypes, we performed RNAseq and ATACseq on control and Dpf2-/- HSCs. Gene Set Enrichment Analyses indicated that Dpf2-/- HSCs have extensive gene expression alterations in immune signaling and interferon response pathways, as well as leukocyte and erythroid differentiation. We also found that Dpf2 loss results in pronounced changes in expression and genomic accessibility of specific transcription factors that control macrophage differentiation and proliferation. Together, our mechanistic studies support a model whereby the absence of Dpf2 results in misregulation of the transcription factor networks that establish macrophage cell identity, leading to a marked increase in macrophage infiltrations and shortened survival of the mice. Treatment of the Dpf2-/-mice with clodronate-containing liposomes, which deplete macrophages from bone marrow and spleen, prolonged survival of the mice. Our work uncovers a novel role of Dpf2 in restraining inflammatory responses by controlling macrophage proliferation and function. Moreover, we propose that, in addition to their tumor suppressive roles in cancer, BAF complexes may have a central role in the prevention of immunopathologies. Disclosures Kadoch: Foghorn Therapeutics: Consultancy, Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees, Other: Scientific founder, fiduciary board of directors member, scientific advisory board member, shareholder, and consultant for Foghorn Therapeutics (Cambridge, MA). . Vega:NCI: Research Funding.

Published
2020

50. Genomic Predictors of Recurrence Patterns After Complete Resection of Colorectal Liver Metastases and Adjuvant Hepatic Artery Infusion Chemotherapy

Author

Narayan, Raja R., Datta, Jashodeep, Goldman, Debra A., Aveson, Victoria G., Walch, Henry S., Sanchez-Vega, Francisco, Gönen, Mithat, Balachandran, Vinod P., Drebin, Jeffrey A., Jarnagin, William R., Kingham, T. Peter, Wei, Alice C., Schultz, Nikolaus, Kemeny, Nancy E., and D’Angelica, Michael I.

Published
2022
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