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Directed discovery of high-loading nanoaggregates enabled by drug-matched oligo-peptide excipients

Chem 2025年

作者： Berisha, Naxhije Farahpour, Atena Ramakrishnan, Maithreyi Chen, Chen McPhee, Scott A. Wang, Tong Li, Tai-De Hema, Kuntrapakam Panagiotakopoulou, Magdalini Athiyarath, Vignesh Coste, Maeva Marciano, Yaron Sherman, Emmet Ulijn, Rein V. Heller, Daniel A. Nanoscience Initiative Advanced Science Research Center CUNY Graduate Center City University of New York New York 10031 NY United States Department of Chemistry and Biochemistry Hunter College City University of New York New York 10065 NY United States PhD Program in Chemistry CUNY Graduate Center City University of New York New York 10016 NY United States Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center New York 10065 NY United States Tri-Institutional PhD Program in Chemical Biology Memorial Sloan Kettering Cancer Center New York 10065 NY United States Department of Physics City College of New York City University of New York New York 10031 NY United States Department of Chemistry Brooklyn College City University of New York 2900 Bedford Avenue Brooklyn 11210 NY United States PhD Program in Biochemistry CUNY Graduate Center City University of New York New York 10016 NY United States Weill Cornell Medicine Cornell University New York 10065 NY United States

Nanoparticles can improve drug pharmacokinetics, but low loading efficiencies can limit treatment efficacy. Drug-aggregation-based nanoparticles have demonstrated improved loadings of up to 90%, but few excipients facilitate efficient co-assembly. We investigated peptides as designer excipients because of their diverse chemical space and inherent biodegradability. We designed pentapeptide scaffolds to mimic the structure of known indocyanine excipients by modulating aromaticity, rigidity, and charge. We screened 184 formulations by using diverse drug cargoes. We found drug-peptide combinations that formed nanoparticles with up to 98% drug loading. Molecular dynamics simulations and mass spectrometry analysis demonstrated that tryptophan-drug interactions and solvent exposure of charged amino acid residues drove the formation of core-shell structures. Peptide-drug formulations containing the JAK2/FLT3 inhibitor lestaurtinib were investigated in acute myeloid leukemia models, resulting in enhanced anti-tumor efficacy. This work found that oligopeptides can be designed to efficiently co-assemble with therapeutic cargoes to result in high-loading nanoparticles that improve anti-tumor efficacy. © 2024

关键词： co-assembly directed discovery drug delivery excipient nanocarrier design nanoparticle oligopeptides SDG3: Good health and well-being

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Space mishap as a stimulus context for thermal conduction exploration in secondary school

Space mishap as a stimulus context for thermal conduction ex...

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GIREP-ICPE-EPEC 2017 Conference

作者： Komáromi, A. Physics Education PhD Program of Eötvös University Budapest Hungary

A large body of literature underlines the relevance of personal involvement and in-context assignments in increasing student engagement in physics education at secondary level. The research-based teaching/learning experience offers different kinds of suggestions for physics education on the level of curricular proposals, on the level of feasibility of inquiry-based learning approaches, on the level of strategies and methods for learning environment settings, and on the level of conceptual understanding of students. During the activities, students find a good opportunity to discuss how heat is transferred, both on Earth and in space. Students discover through their own exploration what types of radiation space objects are exposed to in near-Earth orbits. By means of a "flipped classroom" methodology the students analyse radiant heat absorption and reflection. The activity was extended to learn about heat radiation incident on Earth and emitted by Earth. It was interesting to see the reaction of students when they realized that "radiant heat" has a wavelength, and that it is part of the electromagnetic wave spectrum. Tutorials and post-tests were used in order to gauge the students' understanding of the processes involved, and in particular what their conception of heat is. Students proposed different materials for heat shields used in the experiment, and in this way we touched on the subjects of thermal insulation and heat capacity. This leads us to examine the inner structure of materials, and essentially the link between macro- and micro-world. Discussion of heat absorption is a way to introduce the concept of energy, and consequently the role of macro-micro models in material science processes description. Characteristics and main results of the intervention module will be presented together with data of the monitored learning process. © Published under licence by IOP Publishing Ltd.

关键词： Students

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Deep learning models of the retinal response to natural scenes 30

Deep learning models of the retinal response to natural scen...

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30th Annual Conference on Neural Information Processing Systems, NIPS 2016

作者： McIntosh, Lane T. Maheswaranathan, Niru Nayebi, Aran Ganguli, Surya Baccus, Stephen A. Neurosciences PhD Program United States Department of Applied Physics Mexico Neurobiology Department Stanford University United States

A central challenge in sensory neuroscience is to understand neural computations and circuit mechanisms that underlie the encoding of ethologically relevant, natural stimuli. In multilayered neural circuits, nonlinear processes such as synaptic transmission and spiking dynamics present a significant obstacle to the creation of accurate computational models of responses to natural stimuli. Here we demonstrate that deep convolutional neural networks (CNNs) capture retinal responses to natural scenes nearly to within the variability of a cell's response, and are markedly more accurate than linear-nonlinear (LN) models and Generalized Linear Models (GLMs). Moreover, we find two additional surprising properties of CNNs: they are less susceptible to overfitting than their LN counterparts when trained on small amounts of data, and generalize better when tested on stimuli drawn from a different distribution (e.g. between natural scenes and white noise). An examination of the learned CNNs reveals several properties. First, a richer set of feature maps is necessary for predicting the responses to natural scenes compared to white noise. Second, temporally precise responses to slowly varying inputs originate from feedforward inhibition, similar to known retinal mechanisms. Third, the injection of latent noise sources in intermediate layers enables our model to capture the sub-Poisson spiking variability observed in retinal ganglion cells. Fourth, augmenting our CNNs with recurrent lateral connections enables them to capture contrast adaptation as an emergent property of accurately describing retinal responses to natural scenes. These methods can be readily generalized to other sensory modalities and stimulus ensembles. Overall, this work demonstrates that CNNs not only accurately capture sensory circuit responses to natural scenes, but also can yield information about the circuit's internal structure and function. © 2016 NIPS Foundation - All Rights Reserved.

关键词： Deep neural networks

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Minimal frustration underlies the usefulness of incomplete regulatory network models in biology

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Proceedings of the National Academy of Sciences of the United States of America 2023年第1期120卷 e2216109120-e2216109120页

作者： Tripathi, Shubham Kessler, David A. Levine, Herbert PhD Program in Systems Synthetic and Physical Biology Rice University Houston 77005 TX United States Center for Theoretical Biological Physics Northeastern University Boston 02115 MA United States Department of Physics Northeastern University Boston 02115 MA United States Department of Physics Bar-Ilan University Ramat-Gan 52900 Israel

Regulatory networks as large and complex as those implicated in cell-fate choice are expected to exhibit intricate, very high-dimensional dynamics. Cell-fate choice, however, is a macroscopically simple process. Additionally, regulatory network models are almost always incomplete and/or inexact, and do not incorporate all the regulators and interactions that may be involved in cell-fate regulation. In spite of these issues, regulatory network models have proven to be incredibly effective tools for understanding cell-fate choice across contexts and for making useful predictions. Here, we show that minimal frustration-a feature of biological networks across contexts but not of random networks-can compel simple, low-dimensional steady-state behavior even in large and complex networks. Moreover, the steady-state behavior of minimally frustrated networks can be recapitulated by simpler networks such as those lacking many of the nodes and edges and those that treat multiple regulators as one. The present study provides a theoretical explanation for the success of network models in biology and for the challenges in network inference. © 2022 the Author(s).

关键词： cell-fate choice frustration gene regulatory networks network inference sloppiness

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Chaos physics in High School - Challenges in Multimedia Application

Chaos Physics in High School - Challenges in Multimedia Appl...

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GIREP Malta Webinar 2020

作者： Bajkó, Ildikó Szent István High School Budapest Ajtósi Dürer sor 15 Budapest1146 Hungary Physics Education PhD Program Eötvös Loránd University Budapest Hungary

Besides being an active field of research, chaotic phenomena are also encountered in our everyday life, thus it's worth discussing them also in formal education in public schools. This paper presents the authors' experiences in teaching chaos on secondary level. A teaching module that encompasses mechanics lab experiments and numerical simulations of typical chaotic systems have been implemented and evaluated. The module offers a number of multimedia applications whose availability in teacher education is also discussed. © Published under licence by IOP Publishing Ltd.

关键词： Chaotic systems

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Eclipse timing variations in the WD + dM eclipsing binary RR Cae

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Monthly Notices of the Royal Astronomical Society 2023年第4期523卷 5086-5108页

作者： Rattanamala, R. Awiphan, S. Komonjinda, S. Phriksee, A. Sappankum, P. A-Thano, N. Chitchak, S. Rittipruk, P. Sawangwit, U. Poshyachinda, S. Reichart, D.E. Haislip, J.B. PhD Program in Astronomy Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai50200 Thailand Physics and General Science Program Faculty of Science and Technology Nakhon Ratchasima Rajabhat University Nakhon Ratchasima30000 Thailand 260 Moo 4 Donkaew Mae Rim Chiang Mai50180 Thailand Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai50200 Thailand Institute of Astronomy National Tsing Hua University Hsinchu30013 Taiwan Department of Physics Faculty of Science Udon Thani Rajabhat University Udon Thani41000 Thailand Department of Physics and Astronomy University of North Carolina at Chapel Hill Chapel HillNC27599 United States

We present the binary model and the eclipse timing variations of the eclipsing binary RR Cae, which consists of a white dwarf eclipsed by an M-type dwarf companion. The multiwavelength optical photometry from the Transiting Exoplanet Survey Satellite (TESS), the 0.6-m PROMPT-8 telescope, and the 0.7-m Thai Robotic Telescope at Spring Brook Observatory, combined with archive H α radial velocities from the Very Large Telescope (VLT) are analysed. From the data, the physical parameters of the system are obtained along with 430 new times of minima. The TESS light curves in 2018 and 2020 show out-of-eclipse variations, which might be caused by a large spot on the secondary component. The light travel time effect models due to the gravitational interaction of one or two circumbinary objects are adopted to fit the cyclic variations in the RR Cae’s O-C curve. The fitting solution of the O-C curve with one circumbinary object model shows a periodic variation with a period of 16.6 ± 0.2 yr and an amplitude of 14 ± 1 s, which can be caused by a planet with a minimum mass of 3.4 ± 0.2 MJup. When we consider the model with two circumbinary objects, the O-C curve shows cyclic variations with periods of 15.0 ± 0.5 yr and 39 ± 5 yr and amplitudes of 12 ± 1 s and 20 ± 5 s, respectively, corresponding to minimum masses of 3.0 ± 0.3 MJup and 2.7 ± 0.7 MJup © 2023 The Author(s) Published by Oxford University Press on behalf of Royal Astronomical Society.

关键词： Travel time

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Conditions of the fuzzy internet mortgage market submodels implementation

Frontiers in Artificial Intelligence and Applications

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Frontiers in Artificial Intelligence and Applications 2012年 243卷 1470-1479页

作者： Orlowski, Aleksander Szczerbicki, Edward Gdansk University of Technology Faculty of Applied Physics Mathematics PhD Program Poland Gdansk University of Technology Faculty of Management and Economics Poland

ISBN: (纸本)9781614991045

The paper introduces some challenges of the fast growing mortgage market in Poland, being also the next step of research presented in previous publications, showing the complete process of building and verifying three submodels for the internet mortgage market. The sub-models are described for three market situations, i.e. stable market, crisis, and boom, then the variables within the models are analyzed statistically (e.g. correlation level) and finally the models are verified. The paper presents the process of verification of submodel nr 3 (fast growing market) as an example of the verification process that was applied. The paper concludes with directions for further research in this area leading to the ultimate application of the proposed model in a real life prognosis process. © 2012 The authors and IOS Press. All rights reserved.

关键词： Fuzzy logic

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Biologically inspired protection of deep networks from adversarial attacks

arXiv

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arXiv 2017年

作者： Nayebi, Aran Ganguli, Surya Neurosciences PhD Program Stanford University United States Department of Applied Physics Stanford University United States

Inspired by biophysical principles underlying nonlinear dendritic computation in neural circuits, we develop a scheme to train deep neural networks to make them robust to adversarial attacks. Our scheme generates highly nonlinear, saturated neural networks that achieve state of the art performance on gradient based adversarial examples on MNIST, despite never being exposed to adversarially chosen examples during training. Moreover, these networks exhibit unprecedented robustness to targeted, iterative schemes for generating adversarial examples, including second-order methods. We further identify principles governing how these networks achieve their robustness, drawing on methods from information geometry. We find these networks progressively create highly flat and compressed internal representations that are sensitive to very few input dimensions, while still solving the task. Moreover, they employ highly kurtotic weight distributions, also found in the brain, and we demonstrate how such kurtosis can protect even linear classifiers from adversarial attack. Copyright © 2017, The Authors. All rights reserved.

关键词： Deep neural networks

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Deep learning models of the retinal response to natural scenes

arXiv

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arXiv 2017年

作者： McIntosh, Lane T. Maheswaranathan, Niru Nayebi, Aran Ganguli, Surya Baccus, Stephen A. Neurosciences PhD Program Singapore Department of Applied Physics Singapore Neurobiology Department Stanford University United States

关键词： Ophthalmology

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Toward smart decision support system for Mortgage Market

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Systems Science 2010年第1期36卷 35-40页

作者： OrLowski, Aleksander Szczerbicki, Edward Gdańsk University of Technology Faculty of Applied Physics and Mathematics PhD Program Poland Gdańsk University of Technology Faculty of Management and Economics Poland

This paper presents the structure of initial fuzzy model representing the Polish Internet Mortgage Market. It starts with an introduction describing the market complexities and challenges, and description of previously created rule based model. Then the steps of the process of proposed model fuzzification are presented. Next, there is presented Graphic User Interface developed for the model created. The final part of the paper consists of conclusions and directions for future research.

关键词： Decision support systems

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