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IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

作者： Gil Alterovitz Marco F. Ramon Health Science and Technology/Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge USA Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology / Harvard Medical School- Partners Center for Genetics and Genomics Boston 02115 USA.

High-throughput generation of new types of relational biological datasets is creating a demand for network-based signal processing and pattern recognition to provide new insights. Such networks are often too large to interpret visually and too complicated to be explained solely based on local topological properties. Just as signal processing and statistical techniques have been used in traditional, sequential-based biological datasets, so too are methodologies needed to automatically discern patterns in the huge, emerging networks. One way to do this is by transforming these very large networks into discernable epitomes, or abstracts, of the original networks. This work presents an approach for doing this via topological compression. Through capturing nodes' global topologies and subsequent compression, a new network epitome can be derived. Here, this is done with an E. Coli gene regulation network, resulting in biological findings that could not be derived from the local topology of the original network.

关键词： Biological information theory Network topology Genomics Bioinformatics Biomedical signal processing Compression algorithms Visualization Biology Gas insulated transmission lines Computer science

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Gene lethality detection across biological network domains: Hubs versus stochastic global topological analysis

Gene lethality detection across biological network domains: ...

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IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

作者： Gil Alterovitz Vinayak Muralidhar Marco F. Ramoni Health Science and Technology/Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge USA Harvard Medical School-Partners Center for Genetics and Genomics Boston USA Harvard-MIT Division of Health Sciences and Technology Children's Hospital Informatics Program Boston USA

In this paper, we investigate the properties of lethal genes in E. coli, our model organism. Topological analysis of networks of functional interactions among genes has shown that lethal genes share common local connectivity properties. In this paper, we analyze cellular networks across three domains. We show that a stochastic global topological analysis, via random walks, is more effective at predicting gene lethality than simply looking at local topology using the standard hub-based method. We also introduce the possibility of using metabolic pathways to understand lethal genes, as regulating these pathways is among one of the most important functions of the gene-encoded proteins. Additionally, we analyze lethal genes in terms of the Gene Ontology (GO) and find that the graph forms two highly connected clusters that are each GO enriched for specific terms. We also find that lethal metabolic regulators are extremely enriched. Finally, we provide applications of the work and avenues for future research.

关键词： Stochastic processes Proteins Organisms Humans Genomics Bioinformatics Databases Genetics Network topology Production

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Explore space: Integrating space biomedical engineering education and research

Explore space: Integrating space biomedical engineering educ...

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International Astronautical Federation - 55th International Astronautical Congress 2004

作者： Newman, Dava J. Marquez, Jessica J. Wagner, Erika B. Merfeld, Daniel Trotti, Guillermo Department of Aeronautics and Astronautics and Engineering Systems Massachusetts Institute of Technology Cambridge MA United States Technology and Policy Program Massachusetts Institute of Technology Cambridge MA United States Department of Aeronautics and Astronautics Massachusetts Institute of Technology Cambridge MA United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge MA United States Department of Otology and Laryngology Harvard Medical School Jenks Vestibular Physiology Laboratory Massachusetts Bye and Bar Infirmary Boston MA United States Trotti and Associates Inc. Marblehead MA United States

The Explore Space curricular efforts highlight the development of two post-graduate courses, namely, Space Biomedical Engineering and Life Support Systems and Sensori-Neural Systems, developed and taught at the Massachusetts Institute of technology (mit). Innovative, modular curriculum has been developed to coincide with long-duration human spaceflight research areas. Astronaut performance, exercise, revolutionary spacesuit design, and physiological deconditioning of bones, muscles, and the heart provide motivational themes. Selected topics were adapted for use in undergraduate courses and disseminated to hundreds of children through global outreach. Traditional methods of science and engineering education can no longer be the pedagogical model to meet the needs of a generation of students raised in an increasingly visual, interactive information technology (IT) world. Our outreach efforts culminate in the design of an interactive learning environment, the Knowledge Station, which is a high-impact design workstation for one or two users that facilitates immersive learning. Three Explore Space outcomes are to: 1) Provide multi-level space life sciences curriculum, 2) Excite and educate the public about the wonders of science, engineering and medicine by disseminating knowledge gained through research, and 3) Develop a set of innovative pedagogical strategies that implement tested learning principles as a basis for comprehensive educational evaluation.

关键词： Life support systems (spacecraft)

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Automatic acquisition and processing of large sets of holographic measurements in medical research

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2011 SEM Annual Conference on Experimental and Applied Mechanics

作者： Harrington, Ellery Furlong, Cosme Rosowski, John J. Cheng, Jeffrey T. Center for Holographic Studies and Laser Micro-mechaTronics Department of Mechanical Engineering Worcester Polytechnic Institute 100 Institute Rd Worcester MA 01609 United States Eaton-Peabody Laboratory Massachusetts Eye and Ear Infirmary Boston MA 02114 United States Department of Otology and Laryngology Harvard Medical School Boston MA 02114 United States Speech and Hearing Bioscience and Technology Program MIT-Harvard Division of Health Sciences and Technology Cambridge MA 02139 United States

ISBN: (纸本)9781461402275

We are developing an advanced computer-controlled digital opto-electronic holographic system (DOEHS) with the ability to operate in several modalities, including optoelectronic holographic microscopy, lensless digital holography, speckle pattern interferometry, and fringe projection. The DOEHS is being designed for medical applications requiring full-field-of-view information of shape and deformations to aid in the diagnosis and investigation of specific disorders. Particular features of the DOEHS include the capabilities to rapidly acquire and quantitatively process a relatively large amount of interferometric data. Therefore, automatic procedures for acquisition of images or video, computation and application of quality metrics, and phase unwrapping are applied with minimal user interaction. The results are catalogued with relevant metadata in a database allowing for massive analysis and comparison between subjects or patients. Currently, the DOEHS is being developed to measure acoustically induced deformations of the eardrum of several species, including humans. Measurements are used in diagnosing middle-ear conductive disorders and investigating the causes of failure of middle-ear surgical procedures. We present representative measurement procedures and results.

关键词： Deformation

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Single-neuronal predictions of others' beliefs in humans(vol 591, pg 610, 2021)

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NATURE 2023年第7966期618卷 E25-E25页

作者： Jamali, Mohsen Grannan, Benjamin L. Fedorenko, Evelina Saxe, Rebecca Baez-Mendoza, Raymundo Williams, Ziv M. Department of Neurosurgery Massachusetts General Hospital Harvard Medical School Boston MA USA Harvard-MIT Division of Health Sciences and Technology Boston MA USA Program in Neuroscience Harvard Medical School Boston MA USA Brain and Cognitive Sciences Massachusetts Institute of Technology Boston MA USA

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Smartphone-based detection of voice disorders by long-term monitoring of neck acceleration features

Smartphone-based detection of voice disorders by long-term m...

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2013 IEEE International Conference on Body Sensor Networks, BSN 2013

作者： Mehta, Daryush D. Zañartu, Matías Van Stan, Jarrad H. Feng, Shengran W. Cheyne II, Harold A. Hillman, Robert E. Center for Laryngeal Surgery and Voice Rehabilitation Massachusetts General Hospital Boston MA 02114 United States Department of Surgery Harvard Medical School Boston MA 02115 United States Department of Electronic Engineering Universidad Técnica Federico Santa María Valparaíso Chile Communication Sciences and Disorders MGH Institute of Health Professions Boston MA 02129 United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge MA 02139 United States Bioacoustic Research Program Lab. of Ornithology Cornell University Ithaca NY 14853 United States

ISBN: (纸本)9781479903306

Many common voice disorders are chronic or recurring conditions that are likely to result from inefficient and/or abusive patterns of vocal behavior, termed vocal hyperfunction. Thus an ongoing goal in clinical voice assessment is the long-term monitoring of noninvasively derived measures to track hyperfunction. This paper reports on a smartphone-based voice health monitor that records the high-bandwidth accelerometer signal from the neck skin above the collarbone. Data collection is under way from patients with vocal hyperfunction and matched-control subjects to create a dataset designed to identify the best set of diagnostic measures for hyperfunctional patterns of vocal behavior. Vocal status is tracked from neck acceleration using previously-developed vocal dose measures and novel model-based features of glottal airflow estimates. Clinically, the treatment of hyperfunctional disorders would be greatly enhanced by the ability to unobtrusively monitor and quantify detrimental behaviors and, ultimately, to provide real-time biofeedback that could facilitate healthier voice use. © 2013 IEEE.

关键词： Smartphones

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Unveiling theory of mind in large language models: A parallel to single neurons in the human brain

arXiv

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arXiv 2023年

作者： Jamali, Mohsen Williams, Ziv M. Cai, Jing Department of Neurosurgery Massachusetts General Hospital Harvard Medical School BostonMA United States Harvard-MIT Division of Health Sciences and Technology BostonMA United States Harvard Medical School Program in Neuroscience BostonMA United States

With their recent development, large language models (LLMs) have been found to exhibit a certain level of Theory of Mind (ToM), a complex cognitive capacity that is related to our conscious mind and that allows us to infer another's beliefs and perspective. While human ToM capabilities are believed to derive from the neural activity of a broadly interconnected brain network, including that of dorsal medial prefrontal cortex (dmPFC) neurons, the precise processes underlying LLM's capacity for ToM or their similarities with that of humans remains largely unknown. In this study, we drew inspiration from the dmPFC neurons subserving human ToM and employed a similar methodology to examine whether LLMs exhibit comparable characteristics. Surprisingly, our analysis revealed a striking resemblance between the two, as hidden embeddings (artificial neurons) within LLMs started to exhibit significant responsiveness to either true- or false-belief trials, suggesting their ability to represent another's perspective. These artificial embedding responses were closely correlated with the LLMs' performance during the ToM tasks, a property that was dependent on the size of the models. Further, the other's beliefs could be accurately decoded using the entire embeddings, indicating the presence of the embeddings' ToM capability at the population level. Together, our findings revealed an emergent property of LLMs' embeddings that modified their activities in response to ToM features, offering initial evidence of a parallel between the artificial model and neurons in the human brain. © 2023, CC BY-NC-SA.

关键词： Neurons

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Opening keynote luncheon: “The impact of information technology on health care delivery”

Opening keynote luncheon: “The impact of information techno...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： John Glaser J. Craig Venter Angela Belcher David J. Balaban Mara G. Aspinall Kamil Ugurbil Roni Zeiger Dale Wiggins Dean Kamen Emilio Bizzi Hugh Herr Health Services - Siemens Healthcare J. Craig Venter Institute Massachusetts Institute of Technology Amgen Inc On-Q-ity Inc University of Minnesota Google Inc Philips Healthcare Patient Care and Clinical Informatics DEKA Research and Development Corporation MIT's Program of Media Arts and Sciences and The Harvard-MIT Division of Health Sciences and Technology

health care providers are facing unprecedented pressures to reduce the cost of care and improve the quality and safety of care. These pressures are expected to lead to significant changes in the structure of the industry and the means used to reimburse care providers. Information technology (IT) is seen as a critical contributor to efforts to transform health care delivery. Leveraging a foundation of broadly adopted electronic health records, IT will have four core impacts: — Enabli and improving health care processes — Delivering knowledge to care providers — Engaging patients — Enabling sophisticated analyses of treatment effectiveness and efficiency For IT to achieve its potential research and innovation will be required in several areas.

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Profiling metabolome of mouse embryonic cerebrospinal fluid following maternal immune activation

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Journal of Biological Chemistry 2024年第10期300卷 107749-107749页

作者： Petrova, Boryana Lacey, Tiara E. Culhane, Andrew J. Cui, Jin Brook, Jeannette R. Raskind, Alexander Misra, Aditya Lehtinen, Maria K. Kanarek, Naama Department of Pathology Boston Children's Hospital BostonMA United States Harvard Medical School BostonMA United States Graduate Program in Biological and Biomedical Sciences Harvard Medical School BostonMA United States IROA TechnologiesTM LLC Chapel HillNC United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology CambridgeMA United States Broad Institute of Harvard and Massachusetts Institute of Technology CambridgeMA United States

The embryonic cerebrospinal fluid (eCSF) plays an essential role in the development of the central nervous system (CNS), influencing processes from neurogenesis to lifelong cognitive functions. An important process affecting eCSF composition is inflammation. Inflammation during development can be studied using the maternal immune activation (MIA) mouse model, which displays altered cytokine eCSF composition and mimics neurodevelopmental disorders including autism spectrum disorder (ASD). The limited nature of eCSF as a biosample restricts its research and has hindered our understanding of the eCSF's role in brain pathologies. Specifically, investigation of the small molecule composition of the eCSF is lacking, leaving this aspect of eCSF composition under-studied. We report here the eCSF metabolome as a resource for investigating developmental neuropathologies from a metabolic perspective. Our reference metabolome includes comprehensive MS1 and MS2 datasets and evaluates two mouse strains (CD-1 and C57Bl/6) and two developmental time points (E12.5 and E14.5). We illustrate the reference metabolome's utility by using untargeted metabolomics to identify eCSF-specific compositional changes following MIA. We uncover MIA-relevant metabolic pathways as differentially abundant in eCSF and validate changes in glucocorticoid and kynurenine pathways through targeted metabolomics. Our resource can guide future studies into the causes of MIA neuropathology and the impact of eCSF composition on brain development. © 2024 The Authors

关键词： Cerebrospinal fluid

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Probabilistic Genotype-Phenotype Maps Reveal Mutational Robustness of RNA Folding, Spin Glasses, and Quantum Circuits

arXiv

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arXiv 2023年

作者： Sappington, Anna Mohanty, Vaibhav Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States Program for Health Sciences and Technology Harvard Medical School BostonMA02115 United States Massachusetts Institute of Technology CambridgeMA02139 United States Harvard/MIT MD-PhD Program Harvard Medical School BostonMA02115 United States Department of Chemistry and Chemical Biology Harvard University CambridgeMA02138 United States

Recent studies of genotype-phenotype (GP) maps have reported universally enhanced phenotypic robustness to genotype mutations, a feature essential to evolution. Virtually all of these studies make a simplifying assumption that each genotype—represented as a sequence—maps deterministically to a single phenotype, such as a discrete structure. Here, we introduce probabilistic genotype-phenotype (PrGP) maps, where each genotype maps to a vector of phenotype probabilities, as a more realistic and universal language for investigating robustness in a variety of physical, biological, and computational systems. We study three model systems to show that PrGP maps offer a generalized framework which can handle uncertainty emerging from various physical sources: (1) thermal fluctuation in RNA folding, (2) external field disorder in spin glass ground state finding, and (3) superposition and entanglement in quantum circuits, which are realized experimentally on IBM quantum computers. In all three cases, we observe a novel biphasic robustness scaling which is enhanced relative to random expectation for more frequent phenotypes and approaches random expectation for less frequent phenotypes. We derive an analytical theory for the behavior of PrGP robustness, and we demonstrate that the theory is highly predictive of empirical robustness. © 2023, CC BY.

关键词： Quantum computers

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