1,048 results match your criteria: "Courant Institute of Mathematical Sciences[Affiliation]"

Purpose: Accurately predicting the expected duration of time until total knee replacement (time-to-TKR) is crucial for patient management and health care planning. Predicting when surgery may be needed, especially within shorter windows like 3 years, allows clinicians to plan timely interventions and health care systems to allocate resources more effectively. Existing models lack the precision for such time-based predictions.

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On the Converse of Pansu's Theorem.

Arch Ration Mech Anal

December 2024

Mathematics Institute, University of Warwick, Coventry, CV4 7AL United Kingdom.

We provide a suitable generalisation of Pansu's differentiability theorem to general Radon measures on Carnot groups and we show that if Lipschitz maps between Carnot groups are Pansu-differentiable almost everywhere for some Radon measures , then must be absolutely continuous with respect to the Haar measure of the group.

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Uncertainty quantification in coupled wildfire-atmosphere simulations at scale.

PNAS Nexus

December 2024

Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA.

Uncertainties in wildfire simulations pose a major challenge for making decisions about fire management, mitigation, and evacuations. However, ensemble calculations to quantify uncertainties are prohibitively expensive with high-fidelity models that are needed to capture today's ever-more intense and severe wildfires. This work shows that surrogate models trained on related data enable scaling multifidelity uncertainty quantification to high-fidelity wildfire simulations of unprecedented scale with billions of degrees of freedom.

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Knowledge about seafloor depth, or bathymetry, is crucial for various marine activities, including scientific research, offshore industry, safety of navigation, and ocean exploration. Mapping the central Arctic Ocean is challenging due to the presence of perennial sea ice, which limits data collection to icebreakers, submarines, and drifting ice stations. The International Bathymetric Chart of the Arctic Ocean (IBCAO) was initiated in 1997 with the goal of updating the Arctic Ocean bathymetric portrayal.

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Transport and energetics of bacterial rectification.

Proc Natl Acad Sci U S A

December 2024

Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455.

Randomly moving active particles can be herded into directed motion by asymmetric geometric structures. Although such a rectification process has been extensively studied due to its fundamental, biological, and technological relevance, a comprehensive understanding of active matter rectification based on single particle dynamics remains elusive. Here, by combining experiments, simulations, and theory, we study the directed transport and energetics of swimming bacteria navigating through funnel-shaped obstacles-a paradigmatic model of rectification of living active matter.

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Frequency analyses of postural sway demonstrate the use of sounds for balance given vestibular loss.

Gait Posture

December 2024

Department of Otolaryngology-Head and Neck Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Ear Institute, New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA.

Purpose: To investigate how adults with unilateral vestibular hypofunction and healthy controls incorporate visual and auditory cues for postural control in an abstract visual environment.

Methods: Participants stood on foam wearing the HTC Vive, observing an immersive 3-wall display of 'stars' that were either static or dynamic (moving front to back at 32 mm, 0.2 Hz) with no sound, static white noise, or moving white noise played via headphones.

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Background: Prediction models based on machine learning (ML) methods are being increasingly developed and adopted in health care. However, these models may be prone to bias and considered unfair if they demonstrate variable performance in population subgroups. An unfair model is of particular concern in bladder cancer, where disparities have been identified in sex and racial subgroups.

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DNA targeting Class 2 CRISPR-Cas effector nucleases, including the well-studied Cas9 proteins, evolved protospacer-adjacent motif (PAM) and guide RNA interactions that sequentially license their binding and cleavage activities at protospacer target sites. Both interactions are nucleic acid sequence specific but function constitutively; thus, they provide intrinsic spatial control over DNA targeting activities but naturally lack temporal control. Here we show that engineered Cas9 fusion proteins which bind to nascent RNAs near a protospacer can facilitate spatiotemporal coupling between transcription and DNA targeting at that protospacer: Transcription-associated Cas9 Targeting (TraCT).

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Organic molecular crystals constitute a class of materials of critical importance in numerous industries. Despite the ubiquity of these systems, our ability to predict molecular crystal structures starting only from a two-dimensional diagram of the constituent compound(s) remains a significant challenge. Most structure-prediction protocols require a customized interatomic interaction model on which the quality of the results can depend sensitively.

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Dynamic or structurally induced ionization is a critical aspect of many physical, chemical, and biological processes. Molecular dynamics (MD) based simulation approaches, specifically constant pH MD methods, have been developed to simulate ionization states of molecules or proteins under experimentally or physiologically relevant conditions. While such approaches are now widely utilized to predict ionization sites of macromolecules or to study physical or biological phenomena, they are often computationally expensive and require long simulation times to converge.

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Dynamical mechanisms of how an RNN keeps a beat, uncovered with a low-dimensional reduced model.

Sci Rep

November 2024

Center for Neural Science and Courant Institute of Mathematical Sciences, New York University, New York, NY, 10003, USA.

Despite music's omnipresence, the specific neural mechanisms responsible for perceiving and anticipating temporal patterns in music are unknown. To study potential mechanisms for keeping time in rhythmic contexts, we train a biologically constrained RNN, with excitatory (E) and inhibitory (I) units, on seven different stimulus tempos (2-8 Hz) on a synchronization and continuation task, a standard experimental paradigm. Our trained RNN generates a network oscillator that uses an input current (context parameter) to control oscillation frequency and replicates key features of neural dynamics observed in neural recordings of monkeys performing the same task.

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Nonlinear parametric models of viscoelastic fluid flows.

R Soc Open Sci

October 2024

Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.

Reduced-order models (ROMs) have been widely adopted in fluid mechanics, particularly in the context of Newtonian fluid flows. These models offer the ability to predict complex dynamics, such as instabilities and oscillations, at a considerably reduced computational cost. In contrast, the reduced-order modelling of non-Newtonian viscoelastic fluid flows remains relatively unexplored.

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We study the dynamics of proliferating cell collectives whose microscopic constituents' growth is inhibited by macroscopic growth-induced stress. Discrete particle simulations of a growing collective show the emergence of concentric-ring patterns in cell size whose spatiotemporal structure is closely tied to the individual cell's stress response. Motivated by these observations, we derive a multiscale continuum theory whose parameters map directly to the discrete model.

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Perceptual tri-stability, measured and fitted as emergent from a model for bistable alternations.

Hear Res

November 2024

Center for Neural Science, New York University, 4 Washington Place, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, NY 10012, USA. Electronic address:

The human auditory system in attempting to decipher ambiguous sounds appears to resort to perceptual exploration as evidenced by multi-stable perceptual alternations. This phenomenon has been widely investigated via the auditory streaming paradigm, employing ABA_ triplet sequences with much research focused on perceptual bi-stability with the alternate percepts as either a single integrated stream or as two simultaneous distinct streams. We extend this inquiry with experiments and modeling to include tri-stable perception.

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Cardiac fluid dynamics fundamentally involves interactions between complex blood flows and the structural deformations of the muscular heart walls and the thin valve leaflets. There has been longstanding scientific, engineering, and medical interest in creating mathematical models of the heart that capture, explain, and predict these fluid-structure interactions (FSIs). However, existing computational models that account for interactions among the blood, the actively contracting myocardium, and the valves are limited in their abilities to predict valve performance, capture fine-scale flow features, or use realistic descriptions of tissue biomechanics.

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Media with correlated disorder display unexpected transport properties, but it is still a challenge to design structures with desired spectral features at scale. In this work, we introduce an optimal formulation of this inverse problem by means of the nonuniform fast Fourier transform, thus arriving at an algorithm capable of generating systems with arbitrary spectral properties, with a computational cost that scales O(NlogN) with system size. The method is extended to accommodate arbitrary real-space interactions, such as short-range repulsion, to simultaneously control short- and long-range correlations.

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Nuclear speckles are nuclear membraneless organelles in higher eukaryotic cells playing a vital role in gene expression. Using an in situ reverse transcription-based sequencing method, we study nuclear speckle-associated human transcripts. Our data indicate the existence of three gene groups whose transcripts demonstrate different speckle localization properties: stably enriched in nuclear speckles, transiently enriched in speckles at the pre-messenger RNA stage, and not enriched.

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A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern.

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Stability in recurrent neural models poses a significant challenge, particularly in developing biologically plausible neurodynamical models that can be seamlessly trained. Traditional cortical circuit models are notoriously difficult to train due to expansive nonlinearities in the dynamical system, leading to an optimization problem with nonlinear stability constraints that are difficult to impose. Conversely, recurrent neural networks (RNNs) excel in tasks involving sequential data but lack biological plausibility and interpretability.

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Accelerating multi-coil MR image reconstruction using weak supervision.

MAGMA

October 2024

Center for Data Science, New York University, 60 Fifth Ave, New York, NY, 10011, USA.

Deep-learning-based MR image reconstruction in settings where large fully sampled dataset collection is infeasible requires methods that effectively use both under-sampled and fully sampled datasets. This paper evaluates a weakly supervised, multi-coil, physics-guided approach to MR image reconstruction, leveraging both dataset types, to improve both the quality and robustness of reconstruction. A physics-guided end-to-end variational network (VarNet) is pretrained in a self-supervised manner using a 4 under-sampled dataset following the self-supervised learning via data undersampling (SSDU) methodology.

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Hopping and crawling DNA-coated colloids.

Proc Natl Acad Sci U S A

October 2024

Department of Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012.

Understanding the motion of particles with multivalent ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or roll, depending on the study. We shed light on this problem by observing DNA-coated colloids diffusing near surfaces coated with complementary strands for a wide array of coating designs.

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Microbial colonization programs are structured by breastfeeding and guide healthy respiratory development.

Cell

September 2024

Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada; Manitoba Interdisciplinary Lactation Centre (MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada. Electronic address:

Article Synopsis
  • The study examined how breastfeeding and microbial colonization in infants are related to respiratory health, specifically asthma risk, by analyzing data from over 2,200 children.
  • Researchers discovered that early cessation of breastfeeding can lead to the early introduction of certain harmful microbes linked to immune issues and asthma, while extended breastfeeding supports healthier microbial development.
  • The findings emphasize the significance of prolonged breastfeeding for better respiratory health in children and point to potential new targets for interventions aimed at preventing asthma.
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Phosphotriesterases (PTEs) represent a class of enzymes capable of efficient neutralization of organophosphates (OPs), a dangerous class of neurotoxic chemicals. PTEs suffer from low catalytic activity, particularly at higher temperatures, due to low thermostability and low solubility. Supercharging, a protein engineering approach via selective mutation of surface residues to charged residues, has been successfully employed to generate proteins with increased solubility and thermostability by promoting charge-charge repulsion between proteins.

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Space Quasi-Periodic Steady Euler Flows Close to the Inviscid Couette Flow.

Arch Ration Mech Anal

September 2024

Dipartimento di Matematica "Federigo Enriques", Università degli Studi di Milano, Via Cesare Saldini 50, 20133 Milan, Italy.

We prove the existence of steady stream functions, solutions for the Euler equation in a vorticity-stream function formulation in the two dimensional channel . These solutions bifurcate from a prescribed shear equilibrium near the Couette flow, whose profile induces finitely many modes of oscillations in the horizontal direction for the linearized problem. Using a Nash-Moser implicit function iterative scheme, near such equilibrium we construct small amplitude, space reversible stream functions, slightly deforming the linear solutions and retaining the horizontal quasi-periodic structure.

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Fixational eye movements alter the number and timing of spikes transmitted from the retina to the brain, but whether these changes enhance or degrade the retinal signal is unclear. To quantify this, we developed a Bayesian method for reconstructing natural images from the recorded spikes of hundreds of retinal ganglion cells (RGCs) in the macaque retina (male), combining a likelihood model for RGC light responses with the natural image prior implicitly embedded in an artificial neural network optimized for denoising. The method matched or surpassed the performance of previous reconstruction algorithms, and provides an interpretable framework for characterizing the retinal signal.

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