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1. Neural Correlates of Augmented Reality Safety Warnings: EEG Analysis of Situational Awareness and Cognitive Performance in Roadway Work Zones

Author

Ardecani, Fatemeh Banani, Kumar, Amit, Sabeti, Sepehr, and Shoghli, Omidreza

Subjects
Computer Science - Human-Computer Interaction, Computer Science - Emerging Technologies
Abstract

Despite the research and implementation efforts involving various safety strategies, protocols, and technologies, work zone crashes and fatalities continue to occur at an alarming rate each year. This study investigates the neurophysiological responses to Augmented Reality safety warnings in roadway work zones under varying workload conditions. Using electroencephalogram (EEG) technology, we objectively assessed situational awareness, attention, and cognitive load in simulated low-intensity (LA) and moderate-intensity (MA) work activities. The research analyzed key EEG indicators including beta, gamma, alpha, and theta waves, as well as various combined wave ratios. Results revealed that AR warnings effectively triggered neurological responses associated with increased situational awareness and attention across both workload conditions. However, significant differences were observed in the timing and intensity of these responses. In the LA condition, peak responses occurred earlier (within 125 ms post-warning) and were more pronounced, suggesting a more robust cognitive response when physical demands were lower. Conversely, the MA condition showed delayed peak responses (125-250 ms post-warning) and more gradual changes, indicating a potential impact of increased physical activity on cognitive processing speed. These findings underscore the importance of considering physical workload when designing AR-based safety systems for roadway work zones. The research contributes to the understanding of how AR can enhance worker safety and provides insights for developing more effective, context-aware safety interventions in high-risk work environments.

Published
2024
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10. Augmented Reality Warnings in Roadway Work Zones: Evaluating the Effect of Modality on Worker Reaction Times

Author

Sabeti, Sepehr, Ardecani, Fatemeh Banani, and Shoghli, Omidreza

Subjects
Computer Science - Human-Computer Interaction, Computer Science - Computer Vision and Pattern Recognition, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Given the aging highway infrastructure requiring extensive rebuilding and enhancements, and the consequent rise in the number of work zones, there is an urgent need to develop advanced safety systems to protect workers. While Augmented Reality (AR) holds significant potential for delivering warnings to workers, its integration into roadway work zones remains relatively unexplored. The primary objective of this study is to improve safety measures within roadway work zones by conducting an extensive analysis of how different combinations of multimodal AR warnings influence the reaction times of workers. This paper addresses this gap through a series of experiments that aim to replicate the distinctive conditions of roadway work zones, both in real-world and virtual reality environments. Our approach comprises three key components: an advanced AR system prototype, a VR simulation of AR functionality within the work zone environment, and the Wizard of Oz technique to synchronize user experiences across experiments. To assess reaction times, we leverage both the simple reaction time (SRT) technique and an innovative vision-based metric that utilizes real-time pose estimation. By conducting five experiments in controlled outdoor work zones and indoor VR settings, our study provides valuable information on how various multimodal AR warnings impact workers reaction times. Furthermore, our findings reveal the disparities in reaction times between VR simulations and real-world scenarios, thereby gauging VR's capability to mirror the dynamics of roadway work zones. Furthermore, our results substantiate the potential and reliability of vision-based reaction time measurements. These insights resonate well with those derived using the SRT technique, underscoring the viability of this approach for tangible real-world uses.

Published
2024
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17. Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing

Author

Levine, Zoë C., Sene, Aita, Mkandawire, Winnie, Deme, Awa B., Ndiaye, Tolla, Sy, Mouhamad, Gaye, Amy, Diedhiou, Younouss, Mbaye, Amadou M., Ndiaye, Ibrahima M., Gomis, Jules, Ndiop, Médoune, Sene, Doudou, Faye Paye, Marietou, MacInnis, Bronwyn L., Schaffner, Stephen F., Park, Daniel J., Badiane, Aida S., Colubri, Andres, Ndiaye, Mouhamadou, Sy, Ngayo, Sabeti, Pardis C., Ndiaye, Daouda, and Siddle, Katherine J.

Published
2024
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18. The effect of hard tissue defects on the clinical outcome of endodontic microsurgery: a systematic review and meta-analysis.

Author

Sabeti, Mohammad, Kharat, Piyusha, Azarpazhooh, Amir, and Ihsan, Mohammad Saqib

Subjects
Evidence-based dentistry, Meta-analysis, Prospective cohort, Surgical endodontics, Systematic review, Humans, Microsurgery, Treatment Outcome, Dental Care
Abstract

OBJECTIVES: The purpose of this systematic review was to appraise the existing literature on the effect of hard tissue defects on the clinical outcome of endodontic microsurgery (EMS). METHODS: MEDLINE (PubMed), Embase, Web of Science, Cochrane Library and grey literature were searched from January 2000 to May 2023. Study selection and data extraction were performed in duplicate. Eligible studies were critically appraised for the risk of bias using the Cochrane Risk of bias tool. The quality of evidence was assessed using GRADE. Review Manager (RevMan Computer program Version 5.4, The Cochrane Collaboration, 2020) was utilized and the Mantel Haenszel fixed or random effects model was applied, depending on the heterogeneity of the studies. Meta-analysis was performed to estimate the Risk ratio (RR) and 95% Confidence Interval (CIs) to correlate the effects of these factors on treatment outcomes. RESULTS: Nineteen studies were included. The EMS overall pooled success rate was 84.5%. Five characteristics of hard tissue were identified. The size of the lesion (Small ≤ 5 mm: 78.4% vs. Large > 5 mm: 63.3%, RR = 1.12, 95% CI 1.00-1.26, P ≤ .05), significantly affected the outcomes of EMS. Endodontic lesions exhibited slightly better outcomes than endodontic-periodontal lesions (81.4% vs. 68.2%, RR = 1.14 95% CI 0.98-1.33, P > .05). Cases with the height of the buccal bone > 3 mm also exhibited slightly better outcomes (91.5% vs. 71.4%, RR = 1.20, 95% CI 0.88-1.62, P > .05). Additionally, through and through lesions exhibited better outcomes when grafting was completed during the EMS procedure both in 2D (RR = 1.12 95% CI 0.97-1.29, P > .05) and 3D evaluation ((RR = 1.28 95% CI 0.69-2.37 P > .05). The overall quality of evidence was graded as low to high. CONCLUSION: With a low to high quality of evidence, the size of the lesion is a key prognostic variable that significantly affects the outcome of EMS, as lesions ≤ 5 mm exhibit better outcomes as compared to larger lesions. CLINICAL SIGNIFICANCE: The presence of hard tissue defects can affect the outcome of endodontic microsurgery (EMS). The presented data can aid the clinicians decision-making process by examining certain pre-operative prognostic variables, when considering EMS as a treatment option. Clinical cases with more favorable hard tissue characteristics lead to a better prognosis in EMS.

Published
2023

19. Multicenter integrated analysis of noncoding CRISPRi screens

Author

Yao, David, Tycko, Josh, Oh, Jin Woo, Bounds, Lexi R., Gosai, Sager J., Lataniotis, Lazaros, Mackay-Smith, Ava, Doughty, Benjamin R., Gabdank, Idan, Schmidt, Henri, Guerrero-Altamirano, Tania, Siklenka, Keith, Guo, Katherine, White, Alexander D., Youngworth, Ingrid, Andreeva, Kalina, Ren, Xingjie, Barrera, Alejandro, Luo, Yunhai, Yardımcı, Galip Gürkan, Tewhey, Ryan, Kundaje, Anshul, Greenleaf, William J., Sabeti, Pardis C., Leslie, Christina, Pritykin, Yuri, Moore, Jill E., Beer, Michael A., Gersbach, Charles A., Reddy, Timothy E., Shen, Yin, Engreitz, Jesse M., Bassik, Michael C., and Reilly, Steven K.

Published
2024
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21. Text Representation Enrichment Utilizing Graph based Approaches: Stock Market Technical Analysis Case Study

Author

Salamat, Sara, Tavassoli, Nima, Sabeti, Behnam, and Fahmi, Reza

Subjects
Computer Science - Machine Learning, Quantitative Finance - Computational Finance
Abstract

Graph neural networks (GNNs) have been utilized for various natural language processing (NLP) tasks lately. The ability to encode corpus-wide features in graph representation made GNN models popular in various tasks such as document classification. One major shortcoming of such models is that they mainly work on homogeneous graphs, while representing text datasets as graphs requires several node types which leads to a heterogeneous schema. In this paper, we propose a transductive hybrid approach composed of an unsupervised node representation learning model followed by a node classification/edge prediction model. The proposed model is capable of processing heterogeneous graphs to produce unified node embeddings which are then utilized for node classification or link prediction as the downstream task. The proposed model is developed to classify stock market technical analysis reports, which to our knowledge is the first work in this domain. Experiments, which are carried away using a constructed dataset, demonstrate the ability of the model in embedding extraction and the downstream tasks.

Published
2022

22. A genomic timescale for placental mammal evolution

Author

Foley, Nicole M, Mason, Victor C, Harris, Andrew J, Bredemeyer, Kevin R, Damas, Joana, Lewin, Harris A, Eizirik, Eduardo, Gatesy, John, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Springer, Mark S, Murphy, William J, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Fan, Kaili, Fanter, Cornelia, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, Sullivan, Patrick F, and Sundström, Elisabeth

Subjects
Genetics, Human Genome, Biotechnology, Animals, Female, Biological Evolution, Eutheria, Evolution, Molecular, Fossils, Genomics, Phylogeny, Genetic Variation, Time Factors, Zoonomia Consortium‡, General Science & Technology
Abstract

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.

Published
2023

23. Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs

Author

Moon, Katherine L, Huson, Heather J, Morrill, Kathleen, Wang, Ming-Shan, Li, Xue, Srikanth, Krishnamoorthy, Lindblad-Toh, Kerstin, Svenson, Gavin J, Karlsson, Elinor K, Shapiro, Beth, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, Sullivan, Patrick F, Sundström, Elisabeth, Supple, Megan A, and Swofford, Ross

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Animals, Dogs, Male, Genome, Genomics, Genotype, Phenotype, Wolves, Biodiversity, Genetic Variation, Zoonomia Consortium, General Science & Technology
Abstract

We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.

Published
2023

24. The contribution of historical processes to contemporary extinction risk in placental mammals

Author

Wilder, Aryn P, Supple, Megan A, Subramanian, Ayshwarya, Mudide, Anish, Swofford, Ross, Serres-Armero, Aitor, Steiner, Cynthia, Koepfli, Klaus-Peter, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Marques-Bonet, Tomas, Munoz Fuentes, Violeta, Foley, Kathleen, Meyer, Wynn K, Ryder, Oliver A, Shapiro, Beth, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Mason, Victor C, Meadows, Jennifer RS, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Smit, Arian FA, Springer, Mark, and Srinivasan, Chaitanya

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Behavioral and Social Science, Human Genome, Basic Behavioral and Social Science, Life on Land, Animals, Female, Pregnancy, Eutheria, Extinction, Biological, Genetic Variation, Genome, Population Density, Risk, Zoonomia Consortium‡, General Science & Technology
Abstract

Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.

Published
2023

25. The functional and evolutionary impacts of human-specific deletions in conserved elements

Author

Xue, James R, Mackay-Smith, Ava, Mouri, Kousuke, Garcia, Meilin Fernandez, Dong, Michael X, Akers, Jared F, Noble, Mark, Li, Xue, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Noonan, James P, Capellini, Terence D, Brennand, Kristen J, Tewhey, Ryan, Sabeti, Pardis C, Reilly, Steven K, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, and Steiner, Cynthia

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Neurosciences, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Neurological, Humans, Conserved Sequence, Evolution, Molecular, Genome, Genomics, RNA-Binding Proteins, Sequence Deletion, Brain, Gene Expression Regulation, Developmental, Zoonomia Consortium†, General Science & Technology
Abstract

Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.

Published
2023

26. Integrating gene annotation with orthology inference at scale

Author

Kirilenko, Bogdan M, Munegowda, Chetan, Osipova, Ekaterina, Jebb, David, Sharma, Virag, Blumer, Moritz, Morales, Ariadna E, Ahmed, Alexis-Walid, Kontopoulos, Dimitrios-Georgios, Hilgers, Leon, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Hiller, Michael, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, and Sullivan, Patrick F

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Animals, Female, Mice, Eutheria, Genome, Genomics, Molecular Sequence Annotation, Birds, Zoonomia Consortium‡, General Science & Technology
Abstract

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.

Published
2023

27. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

Author

Kaplow, Irene M, Lawler, Alyssa J, Schäffer, Daniel E, Srinivasan, Chaitanya, Sestili, Heather H, Wirthlin, Morgan E, Phan, BaDoi N, Prasad, Kavya, Brown, Ashley R, Zhang, Xiaomeng, Foley, Kathleen, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Meyer, Wynn K, Pfenning, Andreas R, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, and Steiner, Cynthia

Subjects
Biological Sciences, Genetics, Pediatric, Human Genome, Rare Diseases, Congenital Structural Anomalies, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Mental health, Animals, Enhancer Elements, Genetic, Genetic Variation, Machine Learning, Mammals, Phenotype, Zoonomia Consortium**, General Science & Technology
Abstract

Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.

Published
2023

28. Three-dimensional genome rewiring in loci with human accelerated regions

Author

Keough, Kathleen C, Whalen, Sean, Inoue, Fumitaka, Przytycki, Pawel F, Fair, Tyler, Deng, Chengyu, Steyert, Marilyn, Ryu, Hane, Lindblad-Toh, Kerstin, Karlsson, Elinor, Nowakowski, Tomasz, Ahituv, Nadav, Pollen, Alex, Pollard, Katherine S, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Karlsson, Elinor K, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, and Sullivan, Kevin AM

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Stem Cell Research, Human Genome, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Animals, Humans, Chromatin, Genome, Human, Genomics, Pan troglodytes, Genetic Loci, Neurogenesis, Deep Learning, Zoonomia Consortium§, General Science & Technology
Abstract

Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.

Published
2023

29. Evolutionary constraint and innovation across hundreds of placental mammals

Author

Christmas, Matthew J, Kaplow, Irene M, Genereux, Diane P, Dong, Michael X, Hughes, Graham M, Li, Xue, Sullivan, Patrick F, Hindle, Allyson G, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Breit, Ana M, Diekhans, Mark, Fanter, Cornelia, Foley, Nicole M, Goodman, Daniel B, Goodman, Linda, Keough, Kathleen C, Kirilenko, Bogdan, Kowalczyk, Amanda, Lawless, Colleen, Lind, Abigail L, Meadows, Jennifer RS, Moreira, Lucas R, Redlich, Ruby W, Ryan, Louise, Swofford, Ross, Valenzuela, Alejandro, Wagner, Franziska, Wallerman, Ola, Brown, Ashley R, Damas, Joana, Fan, Kaili, Gatesy, John, Grimshaw, Jenna, Johnson, Jeremy, Kozyrev, Sergey V, Lawler, Alyssa J, Marinescu, Voichita D, Morrill, Kathleen M, Osmanski, Austin, Paulat, Nicole S, Phan, BaDoi N, Reilly, Steven K, Schäffer, Daniel E, Steiner, Cynthia, Supple, Megan A, Wilder, Aryn P, Wirthlin, Morgan E, Xue, James R, Birren, Bruce W, Gazal, Steven, Hubley, Robert M, Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Meyer, Wynn K, Nweeia, Martin, Sabeti, Pardis C, Shapiro, Beth, Smit, Arian FA, Springer, Mark S, Teeling, Emma C, Weng, Zhiping, Hiller, Michael, Levesque, Danielle L, Lewin, Harris A, Murphy, William J, Navarro, Arcadi, Paten, Benedict, Pollard, Katherine S, Ray, David A, Ruf, Irina, Ryder, Oliver A, Pfenning, Andreas R, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Bredemeyer, Kevin R, Clawson, Hiram, Di Palma, Federica, Eizirik, Eduardo, Forsberg-Nilsson, Karin, Garcia, Carlos J, and Halsey, Michaela K

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Generic health relevance, Animals, Female, Humans, Conserved Sequence, Eutheria, Evolution, Molecular, Genome, Human, Zoonomia Consortium§, General Science & Technology
Abstract

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

Published
2023

30. Recommendations on data sharing in HIV drug resistance research

Author

Inzaule, Seth C, Siedner, Mark J, Little, Susan J, Avila-Rios, Santiago, Ayitewala, Alisen, Bosch, Ronald J, Calvez, Vincent, Ceccherini-Silberstein, Francesca, Charpentier, Charlotte, Descamps, Diane, Eshleman, Susan H, Fokam, Joseph, Frenkel, Lisa M, Gupta, Ravindra K, Ioannidis, John PA, Kaleebu, Pontiano, Kantor, Rami, Kassaye, Seble G, Pond, Sergei L Kosakovsky, Kouamou, Vinie, Kouyos, Roger D, Kuritzkes, Daniel R, Lessells, Richard, Marcelin, Anne-Genevieve, Mbuagbaw, Lawrence, Minalga, Brian, Ndembi, Nicaise, Neher, Richard A, Paredes, Roger, Pillay, Deenan, Raizes, Elliot G, Rhee, Soo-Yon, Richman, Douglas D, Ruxrungtham, Kiat, Sabeti, Pardis C, Schapiro, Jonathan M, Sirivichayakul, Sunee, Steegen, Kim, Sugiura, Wataru, van Zyl, Gert U, Vandamme, Anne-Mieke, Wensing, Annemarie MJ, Wertheim, Joel O, Gunthard, Huldrych F, Jordan, Michael R, and Shafer, Robert W

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Antimicrobial Resistance, Sexually Transmitted Infections, Infectious Diseases, HIV/AIDS, 5.1 Pharmaceuticals, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, Humans, HIV Infections, Phylogeny, HIV-1, Drug Resistance, Viral, Anti-Retroviral Agents, Mutation, Anti-HIV Agents, Medical and Health Sciences, General & Internal Medicine, Biomedical and clinical sciences, Health sciences
Abstract

• Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens.  • HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens.  • Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines.  • Although HIV drug resistance data are collected in many studies, such data are often not publicly shared, prompting the need to recommend best practices to encourage and standardize HIV drug resistance data sharing.  • In contrast to other viruses, sharing HIV sequences from phylogenetic studies of transmission dynamics requires additional precautions as HIV transmission is criminalized in many countries and regions.  • Our recommendations are designed to ensure that the data that contribute to HIV drug resistance knowledge will be available without undue hardship to those publishing HIV drug resistance studies and without risk to people living with HIV.

Published
2023

31. Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever

Author

Kotliar, Dylan, Raju, Siddharth, Tabrizi, Shervin, Odia, Ikponmwosa, Goba, Augustine, Momoh, Mambu, Sandi, John Demby, Nair, Parvathy, Phelan, Eric, Tariyal, Ridhi, Eromon, Philomena E., Mehta, Samar, Robles-Sikisaka, Refugio, Siddle, Katherine J., Stremlau, Matt, Jalloh, Simbirie, Gire, Stephen K., Winnicki, Sarah, Chak, Bridget, Schaffner, Stephen F., Pauthner, Matthias, Karlsson, Elinor K., Chapin, Sarah R., Kennedy, Sharon G., Branco, Luis M., Kanneh, Lansana, Vitti, Joseph J., Broodie, Nisha, Gladden-Young, Adrianne, Omoniwa, Omowunmi, Jiang, Pan-Pan, Yozwiak, Nathan, Heuklom, Shannon, Moses, Lina M., Akpede, George O., Asogun, Danny A., Rubins, Kathleen, Kales, Susan, Happi, Anise N., Iruolagbe, Christopher O., Dic-Ijiewere, Mercy, Iraoyah, Kelly, Osazuwa, Omoregie O., Okonkwo, Alexander K., Kunz, Stefan, McCormick, Joseph B., Khan, S. Humarr, Honko, Anna N., Lander, Eric S., Oldstone, Michael B. A., Hensley, Lisa, Folarin, Onikepe A., Okogbenin, Sylvanus A., Günther, Stephan, Ollila, Hanna M., Tewhey, Ryan, Okokhere, Peter O., Schieffelin, John S., Andersen, Kristian G., Reilly, Steven K., Grant, Donald S., Garry, Robert F., Barnes, Kayla G., Happi, Christian T., and Sabeti, Pardis C.

Published
2024
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33. An unusual case of granulomatous scleromyxedema.

Author

Michelle, Lauren, Sabeti, Sara, Yale, Katerina, Urso, Brittany, Lee, Bonnie, and Smith, Janellen

Subjects
IVIG, IVIG, intravenous immunoglobulin, primary cutaneous mucinoses, scleromyxedema
Published
2022

39. Data Discovery Using Lossless Compression-Based Sparse Representation

Author

Sabeti, Elyas, Song, Peter X. K., and Hero III, Alfred O.

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

Sparse representation has been widely used in data compression, signal and image denoising, dimensionality reduction and computer vision. While overcomplete dictionaries are required for sparse representation of multidimensional data, orthogonal bases represent one-dimensional data well. In this paper, we propose a data-driven sparse representation using orthonormal bases under the lossless compression constraint. We show that imposing such constraint under the Minimum Description Length (MDL) principle leads to a unique and optimal sparse representation for one-dimensional data, which results in discriminative features useful for data discovery.

Published
2021

42. Individual-level Modeling of COVID-19 Epidemic Risk

Author

Colubri, Andres, Yadav, Kailash, Jha, Abhishek, and Sabeti, Pardis C.

Subjects
Statistics - Applications, Quantitative Biology - Populations and Evolution, Statistics - Computation
Abstract

The ongoing COVID-19 pandemic calls for a multi-faceted public health response comprising complementary interventions to control the spread of the disease while vaccines and therapies are developed. Many of these interventions need to be informed by epidemic risk predictions given available data, including symptoms, contact patterns, and environmental factors. Here we propose a novel probabilistic formalism based on Individual-Level Models (ILMs) that offers rigorous formulas for the probability of infection of individuals, which can be parameterised via Maximum Likelihood Estimation (MLE) applied on compartmental models defined at the population level. We describe an approach where individual data collected in real-time is integrated with overall case counts to update the a predictor of the susceptibility of infection as a function of individual risk factors., Comment: 16 pages, 5 figures. arXiv admin note: text overlap with arXiv:1908.06822 by other authors

Published
2020

43. Pattern-Based Analysis of Time Series: Estimation

Author

Sabeti, Elyas, Song, Peter X. K., and Hero, Alfred O.

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

While Internet of Things (IoT) devices and sensors create continuous streams of information, Big Data infrastructures are deemed to handle the influx of data in real-time. One type of such a continuous stream of information is time series data. Due to the richness of information in time series and inadequacy of summary statistics to encapsulate structures and patterns in such data, development of new approaches to learn time series is of interest. In this paper, we propose a novel method, called pattern tree, to learn patterns in the times-series using a binary-structured tree. While a pattern tree can be used for many purposes such as lossless compression, prediction and anomaly detection, in this paper we focus on its application in time series estimation and forecasting. In comparison to other methods, our proposed pattern tree method improves the mean squared error of estimation.

Published
2020

44. Assessing the Efficiency of Different Control Strategies for the Coronavirus (COVID-19) Epidemic

Author

Castilho, César, Gondim, João A. M., Marchesin, Marcelo, and Sabeti, Mehran

Subjects
Quantitative Biology - Populations and Evolution
Abstract

The goal of this work is to analyse the effects of control policies for the coronavirus (COVID-19) epidemic in Brazil. This is done by considering an age-structured SEIR model with a quarantine class and two types of controls. The first one studies the sensitivity with regard to the parameters of the basic reproductive number R0 which is calculated by the next generation method. The second one evaluates different quarantine strategies by comparing their relative total number of deaths.

Published
2020

45. A unique case of progressive hemifacial microsomia or Parry-Romberg syndrome associated with limb and brain anomalies with normal neurological findings: A review of the literature

Author

Pattnaik, Anandita, Lim, Alexandra, Sabeti, Sara, Kwon, Ashley, Hall, Katherine, Lott, Ira, and Kimonis, Virginia

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Congenital Structural Anomalies, Neurodegenerative, Pain Research, Biomedical Imaging, Clinical Research, Pediatric, Neurosciences, Chronic Pain, Aetiology, 2.1 Biological and endogenous factors, Neurological, Brain, Child, Facial Hemiatrophy, Female, Goldenhar Syndrome, Humans, Limb Deformities, Congenital, Phenotype, Parry-Romberg syndrome, Hemifacial atrophy, Midline indentation, White matter lesions, Genetics, Genetics & Heredity, Clinical sciences
Abstract

In this report, we describe an unusual case of progressive hemifacial atrophy or Parry-Romberg syndrome in a 10-year-old girl with progressive hemifacial microsomia and limb anomalies who had brain magnetic resonance imaging (MRI) findings of white matter hyper-intensities. Patients typically present with neurological manifestations such as epilepsy, facial pain, and migraines and ophthalmological symptoms in conjunction with white matter lesions. The patient demonstrated normal cognition and psychomotor development despite the presence of white matter lesions in her frontal lobe that is commonly associated with neurological symptoms. This report brings attention to the complicated relationship between facial, limb and brain imaging findings in Parry-Romberg syndrome and differentiates it from hemifacial microsomia syndrome.

Published
2021

46. Consensus Statement for the Management and Treatment of Sturge-Weber Syndrome: Neurology, Neuroimaging, and Ophthalmology Recommendations

Author

Sabeti, Sara, Ball, Karen L, Bhattacharya, Sanjoy K, Bitrian, Elena, Blieden, Lauren S, Brandt, James D, Burkhart, Craig, Chugani, Harry T, Falchek, Stephen J, Jain, Badal G, Juhasz, Csaba, Loeb, Jeffrey A, Luat, Aimee, Pinto, Anna, Segal, Eric, Salvin, Jonathan, and Kelly, Kristen M

Subjects
Biomedical and Clinical Sciences, Ophthalmology and Optometry, Brain Disorders, Pediatric, Orphan Drug, Clinical Research, Eye Disease and Disorders of Vision, Congenital Structural Anomalies, Rare Diseases, Biomedical Imaging, Epilepsy, Neurosciences, Neurodegenerative, 4.2 Evaluation of markers and technologies, Neurological, Child, Child, Preschool, Congresses as Topic, Consensus, Glaucoma, Humans, Infant, Infant, Newborn, Neuroimaging, Neurology, Ophthalmology, Port-Wine Stain, Practice Guidelines as Topic, Seizures, Sturge-Weber Syndrome, Consensus statement, Sturge-Weber syndrome, Port-wine birthmark, Paediatrics and Reproductive Medicine, Neurology & Neurosurgery, Paediatrics
Abstract

BackgroundSturge-Weber syndrome (SWS) is a sporadic, neurocutaneous syndrome involving the skin, brain, and eyes. Because of the variability of the clinical manifestations and the lack of prospective studies, consensus recommendations for management and treatment of SWS have not been published.ObjectiveThis article consolidates the current literature with expert opinion to make recommendations to guide the neuroimaging evaluation and the management of the neurological and ophthalmologic features of SWS.MethodsThirteen national peer-recognized experts in neurology, radiology, and ophthalmology with experience treating patients with SWS were assembled. Key topics and questions were formulated for each group and included (1) risk stratification, (2) indications for referral, and (3) optimum treatment strategies. An extensive PubMed search was performed of English language articles published in 2008 to 2018, as well as recent studies identified by the expert panel. The panel made clinical practice recommendations.ConclusionsChildren with a high-risk facial port-wine birthmark (PWB) should be referred to a pediatric neurologist and a pediatric ophthalmologist for baseline evaluation and periodic follow-up. In newborns and infants with a high-risk PWB and no history of seizures or neurological symptoms, routine screening for brain involvement is not recommended, but brain imaging can be performed in select cases. Routine follow-up neuroimaging is not recommended in children with SWS and stable neurocognitive symptoms. The treatment of ophthalmologic complications, such as glaucoma, differs based on the age and clinical presentation of the patient. These recommendations will help facilitate coordinated care for patients with SWS and may improve patient outcomes.

Published
2021

48. Blind Channel Estimation for Massive MIMO: A Deep Learning Assisted Approach

Author

Sabeti, Parna, Farhang, Arman, Macaluso, Irene, Marchetti, Nicola, and Doyle, Linda

Subjects
Electrical Engineering and Systems Science - Signal Processing
Abstract

Large scale multiple-input multiple-output (MIMO) or Massive MIMO is one of the pivotal technologies for future wireless networks. However, the performance of massive MIMO systems heavily relies on accurate channel estimation. While the acquisition of channel state information (CSI) in such systems requires an increasingly large amount of training overhead as the number of users grows. To tackle this issue, in this paper, we propose a deep learning assisted blind channel estimation technique for orthogonal frequency division multiplexing (OFDM) based massive MIMO systems. We prove that by exploiting the asymptotic orthogonality of the massive MIMO channels, the channel distortion can be averaged out without the prior knowledge of channel impulse responses, and after some mathematical manipulation, different users transmitted data symbols can be extracted. Thus, by deploying a denoising convolutional neural network algorithm (DnCNN), we mitigate a remaining channel and noise effect to accurately detect the transmitted data symbols at the channel sounding stage. Using the detected data symbols as virtual pilots, we estimate the CSI of all the users at each BS antennas. Our simulation results testify the efficacy of our proposed technique and demonstrate that it can provide a mean square error (MSE) performance which coincides with that of the data-aided channel estimation technique., Comment: 6 pages and 4 figures

Published
2020

49. Lasers, Birthmarks, and Sturge‐Weber Syndrome: A Pilot Survey

Author

Sabeti, Sara, Tackett, Kelly J, Ball, Karen L, Terrell, Julia, Kelly, Kristen M, and Burkhart, Craig

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Dentistry, Patient Safety, Clinical Research, Cancer, Management of diseases and conditions, 7.1 Individual care needs, Humans, Lasers, Port-Wine Stain, Severity of Illness Index, Sturge-Weber Syndrome, Surveys and Questionnaires, Sturge-Weber syndrome, port-wine birthmark, laser treatment, health belief model, Dermatology & Venereal Diseases, Clinical sciences
Abstract

Background and objectivesThere is limited or no data on the experience of patients with Sturge-Weber Syndrome (SWS) and/or their parents who seek out laser treatments for their port-wine birthmark (PWB). Our study aimed to develop a survey to understand patient perspectives on laser therapy and subsequent behaviors while focusing on three elements of the health belief model: perceived susceptibility, perceived benefits, and perceived barriers.Study design/materials and methodsA 31 item survey was developed and sent to 650 members of the Sturge-Weber Foundation. The survey included questions regarding four domains: demographics, disease severity, laser experience, and perceptions and behaviors. Logistic regression models and bivariate analyses were conducted to analyze the results.ResultsAmong the 123 respondents, earlier initiation of laser treatments was associated with greater birthmark satisfaction. Overall satisfaction increased up to 20 treatments and then leveled off. Color satisfaction increased up to 100 laser treatments; however, the flatness of the PWB was not associated with the number of laser treatments. The perceived benefits of lasers were not associated with the number of lifetime treatments or with spending. However, the perceived susceptibility was associated with greater spending on travel and medical expenses.ConclusionThe results of our survey provide insight into SWS patient experiences, beliefs, and behaviors regarding laser therapy. Further exploration of these variables may allow for the improvement of the care experience. Lasers Surg. Med. © 2020 Wiley Periodicals LLC.

Published
2021

50. Early Release - Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in Patient Receiving Rituximab - Volume 27, Number 1—January 2021 - Emerging Infectious Diseases journal - CDC

Author

Solomon, Isaac H, Ganesh, Vijay S, Yu, Guixia, Deng, Xian Ding, Wilson, Michael R, Miller, Steve, Milligan, Tracey A, Mukerji, Shibani S, Mathewson, Abigail, Linxweiler, Justin, Morse, Darlene, Ritter, Jana M, Staples, J Erin, Hughes, Holly, Gould, Carolyn V, Sabeti, Pardis C, Chiu, Charles Y, and Piantadosi, Anne

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Neurosciences, Good Health and Well Being, Antibodies, Viral, Encephalitis Virus, California, Encephalitis, California, Humans, Male, Metagenome, Metagenomics, Middle Aged, Rituximab, Jamestown Canyon virus, arbovirus, encephalitis, metagenomic next-generation sequencing, monoclonal antibody, orthobunyavirus, rituximab, vector-borne infections, viruses, Medical Microbiology, Public Health and Health Services, Microbiology, Clinical sciences, Epidemiology, Health services and systems
Abstract

A 56-year-old man receiving rituximab who had months of neurologic symptoms was found to have Jamestown Canyon virus in cerebrospinal fluid by clinical metagenomic sequencing. The patient died, and postmortem examination revealed extensive neuropathologic abnormalities. Deep sequencing enabled detailed characterization of viral genomes from the cerebrospinal fluid, cerebellum, and cerebral cortex.

Published
2021

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