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arXiv 2023年

作者： Poldrack, Russell A. Markiewicz, Christopher J. Appelhoff, Stefan Ashar, Yoni K. Auer, Tibor Baillet, Sylvain Bansal, Shashank Beltrachini, Leandro Bénar, Christian G. Bertazzoli, Giacomo Bhogawar, Suyash Blair, Ross W. Bortoletto, Marta Boudreau, Mathieu Brooks, Teon L. Calhoun, Vince D. Castelli, Filippo Maria Clement, Patricia Cohen, Alexander L. Cohen-Adad, Julien D'Ambrosio, Sasha de Hollander, Gilles de la Iglesia-Vayá, María de la Vega, Alejandro Delorme, Arnaud Devinsky, Orrin Draschkow, Dejan Duff, Eugene Paul DuPre, Elizabeth Earl, Eric Esteban, Oscar Feingold, Franklin W. Flandin, Guillaume Galassi, Anthony Gallitto, Giuseppe Ganz, Melanie Gau, Rémi Gholam, James Ghosh, Satrajit S. Giacomel, Alessio Gillman, Ashley G. Gleeson, Padraig Gramfort, Alexandre Guay, Samuel Guidali, Giacomo Halchenko, Yaroslav O. Handwerker, Daniel A. Hardcastle, Nell Herholz, Peer Hermes, Dora Honey, Christopher J. Innis, Robert B. Ioanas, Horea-Ioan Jahn, Andrew Karakuzu, Agah Keator, David B. Kiar, Gregory Kincses, Balint Laird, Angela R. Lau, Jonathan C. Lazari, Alberto Legarreta, Jon Haitz Li, Adam Li, Xiangrui Love, Bradley C. Lu, Hanzhang Maumet, Camille Mazzamuto, Giacomo Meisler, Steven L. Mikkelsen, Mark Mutsaerts, Henk Nichols, Thomas E. Nikolaidis, Aki Nilsonne, Gustav Niso, Guiomar Norgaard, Martin Okell, Thomas W. Oostenveld, Robert Ort, Eduard Park, Patrick J. Pawlik, Mateusz Pernet, Cyril R. Pestilli, Franco Petr, Jan Phillips, Christophe Poline, Jean-Baptiste Pollonini, Luca Raamana, Pradeep Reddy Ritter, Petra Rizzo, Gaia Robbins, Kay A. Rockhill, Alexander P. Rogers, Christine Rokem, Ariel Rorden, Chris Routier, Alexandre Saborit-Torres, Jose Manuel Salo, Taylor Schirner, Michael Smith, Robert E. Spisak, Tamas Sprenger, Julia Swann, Nicole C. Szinte, Martin Takerkart, Sylvain Thirion, Bertrand Thomas, Adam G. Torabian, Sajjad Varoquaux, Gael Voytek, Bradley Welzel, Julius Wilson, Martin Yarkoni, Tal Gorgolewski, Krzysztof J. Department of Psychology Stanford University StanfordCA United States Max Planck Institute for Human Development Berlin Germany University of Colorado Anschutz Medical Campus AuroraCO United States School of Psychology University of Surrey Guildford United Kingdom McConnell Brain Imaging Centre Montréal Neurological Institute McGill University Montréal Canada Department of Bioengineering University of California San Diego La Jolla CA United States School of Physics Astronomy Cardiff University Wales United Kingdom Institut de Neurosciences des Systèmes Marseille France Neurophysiology Lab IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy Center for Mind/Brain Sciences - CIMeC University of Trento TN Rovereto Italy Brigham and Women’s Hospital BostonMA United States Massachusetts General Hospital BostonMA United States Harvard Medical School BostonMA United States Rackspace Technology San AntonioTX United States NeuroPoly Lab Polytechnique Montréal MontréalQC Canada Georgia State Georgia Tech Emory AtlantaGA United States University of Florence Sesto Fiorentino Italy Bioretics srl Cesena Italy Department of Medical Imaging Ghent University Hospital Ghent Belgium Department of Diagnostic Sciences Ghent University Ghent Belgium Department of Neurology Boston Children's Hospital BostonMA United States Dipartimento di Scienze della Salute dell'Università degli Studi di Milano Milan Italy Department of Clinical and Experimental Epilepsy University College London United Kingdom Zurich Center for Neuroeconomics Department of Economics University of Zurich Zurich Switzerland UMIB-FISABIO Valencia Spain The University of Texas at Austin AustinTX United States SCCN University of California San Diego La Jolla CA United States Department of Neurology NYU Langone Medical Center New YorkNY United States Department of Experimental Psychology University of Oxford Oxford United Kingdom UK Dementia Research Ins

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS. © 2023, CC BY.

关键词： Data structures

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Clonal Expansion of Lgr5-Positive Cells from Mammalian Cochlea and High-Purity Generation of Sensory Hair Cells

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CELL REPORTS 2017年第8期18卷 1917-1929页

作者： McLean, Will J. Yin, Xiaolei Lu, Lin Lenz, Danielle R. McLean, Dalton Langer, Robert Karp, Jeffrey M. Edge, Albert S. B. Harvard Med Sch Dept Otol & Laryngol Boston MA 02115 USA Massachusetts Eye & Ear Infirm Eaton Peabody Lab Boston MA 02114 USA Harvard MIT Div Hlth Sci & Technol Program Speech & Hearing Bioscience & Technol Cambridge MA 02139 USA Koch Inst Integrat Canc Res MIT Cambridge MA 02142 USA Brigham & Womens Hosp Div Engn Med Dept Med Boston MA 02115 USA Harvard Med Sch Dept Med Boston MA 02115 USA Harvard Stem Cell Inst Cambridge MA 02138 USA Harvard MIT Div Hlth Sci & Technol Cambridge MA 02139 USA MIT Dept Chem Engn Cambridge MA 02142 USA Frequency Therapeut Woburn MA 01801 USA

Death of cochlear hair cells, which do not regenerate, is a cause of hearing loss in a high percentage of the population. Currently, no approach exists to obtain large numbers of cochlear hair cells. Here, using a small-molecule approach, we show significant expansion(>2,000-fold) of cochlear supporting cells expressing and maintaining Lgr5, an epithelial stem cell marker, in response to stimulation of Wnt signaling by a GSK3 beta inhibitor and transcriptional activation by a histone deacetylase inhibitor. The Lgr5-expressing cells differentiate into hair cells in high yield. From a single mouse cochlea, we obtained over 11,500 hair cells, compared to less than 200 in the absence of induction. The newly generated hair cells have bundles and molecular machinery for transduction, synapse formation, and specialized hair cell activity. Targeting supporting cells capable of proliferation and cochlear hair cell replacement could lead to the discovery of hearing loss treatments.

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Stimulus frequency otoacoustic emission generation within a finite element model of the mouse cochlea: The effect of impedance irregularities of organ of Corti structures

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AIP Conference Proceedings 2018年第1期1965卷

作者： Hamid Motallebzadeh Sunil Puria 1Eaton-Peabody Laboratory Massachusetts Eye and Ear 2Department of Otolaryngology Harvard Medical School 3Speech and Hearing Bioscience and Technology Harvard University Graduate School of Arts and Sciences

Stimulus-Frequency Otoacoustic emissions (SFOAEs) are sounds that are generated by the cochlea and carry signatures of cochlear mechanisms and amplification. Although SFOAEs are not thought to contribute to the sensitivity of the hearing process, they provide valuable non-invasive information about cochlear function and potentially can be used in the clinical assessment of sensory-neural hearing loss. The source of SFOAE is thought to be due to the travelling wave reflected by local impedance roughness which is due to random perturbations of the organ of Corti structures (Shera and Zweig, 1993). While the active process of the outer hair cells (OHCs) tunes the peak of the traveling wave, the source of the random perturbations in generating SFOAEs is not well established. In the present work, random perturbations around baseline model parameters (e.g., Young’s moduli and geometrical parameters of the basilar membrane (BM), reticular lamina (RL), outer hair cells (OHCs) as well as their gain factor (the ratio of the axial force that OHC generates due to the shear force on OHC stereocilia) were studied in a finite-element model of the mouse cochlea. Consistent with experimental measurements, the model successfully produces SFOAE magnitudes and phase delays, without significantly affecting cochlear tuning. The model SFOAE amplitude and phase are more sensitive to perturbations in BM Young’s modulus and thickness and to OHC gain than to RL Young’s modulus and thickness and OHC Young’s moduli. Irregularities of OHC gain factor seems to be a plausible source of the SFOAEs because not only their distribution varies along the cochlear length but also their functionality is vulnerable. The model also confirms that the SFOAE magnitude increases, approximately linearly with the perturbation of BM Young’s modulus.

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Bone-conduction circuit model for chinchilla part I: Defining parameters by fitting to air-conduction data

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AIP Conference Proceedings 2018年第1期1965卷

作者： Peter Bowers John J. Rosowski 1Eaton-Peabody Laboratory Mass. Eye & Ear MA USA 3Speech and Hearing Bioscience and Technology program Harvard and M.I.T. MA USA 2Department of Otology and Laryngology Harvard Medical School MA USA

An air-conduction circuit model that will serve as the basis for a model of bone-conduction hearing is developed for chinchilla. The lumped-element model is based on the classic Zwislocki model of the human middle ear. Model parameters are fit to various measurements of chinchilla middle-ear transfer functions and impedances. The model is in agreement with studies of the effects of middle-ear cavity holes in experiments that require access to the middle-ear air space.

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Impedances of the ear estimated with intracochlear pressures in normal human temporal bones

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AIP Conference Proceedings 2018年第1期1965卷

作者： Darcy Frear Xiying Guan Christof Stieger Hideko Heidi Nakajima 1Speech and Hearing Bioscience and Technology Program Harvard Medical School USA 2Dept. Otolaryngology Massachusetts Eye & Ear Harvard Medical School Boston MA USA 3University Hospital Basel Switzerland 4University Bern Switzerland

We have measured intracochlear pressures and velocities of stapes and round window (RW) evoked by air conduction (AC) stimulation in many fresh human cadaveric specimens. Our techniques have improved through the years to ensure reliable pressure sensor measurements in the scala vestibuli and scala tympani. Using these measurements, we have calculated impedances of the middle and inner ear (cochlear partition, RW, and physiological leakage impedance in scala vestibuli) to create a lumped element model. Our model simulates our data and allows us to understand the mechanisms involved in air-conducted sound transmission. In the future this model will be used as a tool to understand transmission mechanisms of various stimuli and to help create more sophisticated models of the ear.

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The effect of middle ear cavity and superior canal dehiscence on wideband acoustic immittance in fresh human cadaveric specimens

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AIP Conference Proceedings 2018年第1期1965卷

作者： Salwa F. Masud Stefan Raufer Stephen T. Neely Hideko H. Nakajima 1Speech and Hearing Bioscience and Technology Program Harvard Medical School Cambridge MA USA 3Boys Town National Research Hospital Omaha NE USA 2Department of Otolaryngology Harvard Medical School Massachusetts Eye & Ear Boston MA USA

Superior canal dehiscence (SCD) is a hole in the bony wall of the superior semicircular canal, which can cause various auditory and/or vestibular symptoms and can result in wrong and/or delayed diagnosis. Wideband acoustic immittance (WAI) can potentially distinguish various mechanical middle-ear pathologies as well as inner-ear pathologies non-invasively. We found that in patients, SCD was commonly associated with a narrow-band decrease in power reflectance (PR, derived from WAI) near 1 kHz. Because clinical data has large variation across individual ears and because we do not know the individual “normal” state prior to SCD, we measured WAI in five fresh temporal bone specimens to determine the effects of SCD with respect to the normal state. In temporal bone, we measured PR to assess mechanical changes before and after SCD, as well as to assess the effect of an open or closed middle-ear cavity. After SCD, PR had a consistent decrease between 0.48 and 0.76 kHz, and a slight increase between 1.04 and 1.4 kHz in the open cavity condition. However, in several experiments, we observed low PR around 1 kHz in the normal state before SCD, likely due to the specimen’s open middle ear cavity (MEC). Because we see effects of both SCD and open MEC around 1 kHz, some of the SCD effect can be masked by the effect of the MEC in the temporal bone specimens. To compensate for this MEC effect, we estimated the effect of SCD in a closed MEC case, but the effect did not differ significantly from the measured open MEC. This study demonstrates the limitation of temporal bone experiments with open MEC when studying inner-ear lesions with WAI.

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Auditory-nerve phenomena relevant to cochlear mechanics

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AIP Conference Proceedings 2018年第1期1965卷

作者： John J. Guinan, Jr. Hui Nam 1Eaton-Peabody Laboratories Mass. Eye and Ear Infirmary 243 Charles St. Boston MA 02114 USA 2Harvard Medical School Dept. of Otolaryngology Boston MA USA 3Harvard-MIT HST Speech and Hearing Bioscience and Technology Program Cambridge MA. USA

We review auditory-nerve response properties that provide insight into cochlear mechanics with special emphasis on properties that are not well explained by the current understanding of cochlear mechanics.

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Drive mechanisms to the inner and outer hair cell stereocilia

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AIP Conference Proceedings 2018年第1期1965卷

作者： Nima Maftoon Hamid Motallebzadeh John J. Guinan, Jr. Sunil Puria 1Eaton-Peabody Laboratory Massachusetts Eye and Ear Harvard University Graduate School of Arts and Sciences USA 2Department of Otolaryngology Harvard Medical School Harvard University Graduate School of Arts and Sciences USA 3Speech and Hearing Bioscience and Technology Harvard University Graduate School of Arts and Sciences USA

It has been long believed that inner hair cell (IHC) stimulation can be gleaned from the classic ter-Kuile shear motion between the reticular lamina (RL) and tectorial membrane (TM). The present study explores this and other IHC stimulation mechanisms using a finite-element-model representation of an organ of Corti (OoC) cross section with fluid-structure interaction. A 3-D model of a cross section of the OoC including soft tissue and the fluid in the sub-tectorial space, tunnel of Corti and above the TM was formulated based on anatomical measurements from the gerbil apical turn. The outer hair cells (OHCs), Deiter’s cells and their phalangeal processes are represented as Y-shaped building-block elements. Each of the IHC and OHC bundles is represented by a single sterocilium. Linearized Navier-Stokes equations coupled with linear-elastic equations discretized with tetrahedral elements are solved in the frequency domain. We evaluated the dynamic changes in the OoC motion including sub-tectorial gap dimensions for 0.1 to 10 kHz input frequencies. Calculations show the classic ter-Kuile motion but more importantly they show that the gap-height changes which produce oscillatory radial flow in the subtectorial space. Phase changes in the stereocilia across OHC rows and the IHC are also observed.

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Mechano-electro-magnetic finite element model of a balanced armature transducer for a contact hearing aid

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AIP Conference Proceedings 2018年第1期1965卷

作者： Morteza Khaleghi Sunil Puria 1Earlens Corporation Menlo Park CA 94025 USA 2Eaton-Peabody Laboratories Massachusetts Eye and Ear MA USA 3Department of Otolaryngology Harvard Medical School MA USA 4Speech and Hearing Bioscience and Technology Harvard Graduate School of Arts and Sciences MA USA

Balanced Armature Transducers (BAT) are primary components of most of hearing aids. The goal of this work is to report on development and validation of a 2D Multiphysics Finite Element (FE) model of a BAT used in a Contact hearing Aid (CHA). Electrical, magnetic, acoustic, and solid mechanics fields are coupled to simulate the system from electrical input to the coil, all the way to the mechanical vibration of the armature. Results from this model are verified with measurements of the armature’s velocity and electrical impedance, over a frequency range of 0.1 to 10 kHz. In addition, the FE results are compared with a 1D lumped-element two-port model of the isolated BAT (Kim and Allen, 2013). Consistent with the experimental measurements, the BAT’s FE model exhibits the first natural frequency of the armature’s velocity around 3,800 Hz. This frequency is determined by both the primary stiffness of the armature and from a negative stiffness introduced by magnetization of the BAT (i.e., the DC magnetic field from the two permanent magnets located inside the BAT). This model paves the path towards the numerical investigation and improvement of the BAT’s design parameters including the number of turns and wire gauge diameter of the coil, geometrical (the thickness and its geometry) and material (density and elastic modulus) properties of the armature, and the magnetic properties of the armature and casing that houses the BAT.

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The pectinate zone is stiff and the arcuate zone determines passive basilar membrane mechanics in the gerbil

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AIP Conference Proceedings 2018年第1期1965卷

作者： Hongyi Xia Charles R. Steele Sunil Puria 1Department of Mechanical Engineering Stanford University CA USA 2Eaton-Peabody Laboratories Massachusetts Eye and Ear Infirmary MA USA 3Department of Otolaryngology Harvard Medical School MA USA 4Speech and Hearing Bioscience and Technology Harvard University Graduate School of Arts and Sciences USA

The gerbil basilar membrane (BM) differs from other mammalian BMs in that the lower collagen-fiber layer of the pectinate zone (PZ) forms an arch, the upper fiber layer is flat, and ground substance separates the two layers. The role of this arch has been unknown, but can be elucidated by models. In the standard simple beam model (SBM), the upper and lower collagen-fiber layers of the BM are represented as a single layer in both the PZ and the arcuate zone (AZ). In our new arch-beam model (ABM), the upper fiber layer is flat, the lower layer forms an arch in the PZ, and the two layers combine to form the flat portion of the BM in the AZ. This design is incorporated into a 3D finite-element tapered-box model of the cochlea with viscous fluid. We find in the model that the PZ rotates as a rigid body, so its specific properties have little influence, while the AZ thickness and collagen volume fraction primarily determine passive BM mechanics.

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