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1. Type 2 diabetes mellitus accelerates brain aging and cognitive decline: Complementary findings from UK Biobank and meta-analyses

   https://doi.org/10.7554/eLife.73138  

   Antal, Botond ; McMahon, Liam P ; Sultan, Syed Fahad ; Lithen, Andrew ; Wexler, Deborah J ; Dickerson, Bradford ; Ratai, Eva-Maria ; Mujica-Parodi, Lilianne R ( May 2022 , eLife)

   Background: Type 2 diabetes mellitus (T2DM) is known to be associated with neurobiological and cognitive deficits; however, their extent, overlap with aging effects, and the effectiveness of existing treatments in the context of the brain are currently unknown. Methods: We characterized neurocognitive effects independently associated with T2DM and age in a large cohort of human subjects from the UK Biobank with cross-sectional neuroimaging and cognitive data. We then proceeded to evaluate the extent of overlap between the effects related to T2DM and age by applying correlation measures to the separately characterized neurocognitive changes. Our findings were complemented by meta-analyses of published reports with cognitive or neuroimaging measures for T2DM and healthy controls (HCs). We also evaluated in a cohort of T2DM-diagnosed individuals using UK Biobank how disease chronicity and metformin treatment interact with the identified neurocognitive effects. Results: The UK Biobank dataset included cognitive and neuroimaging data (N = 20,314), including 1012 T2DM and 19,302 HCs, aged between 50 and 80 years. Duration of T2DM ranged from 0 to 31 years (mean 8.5 ± 6.1 years); 498 were treated with metformin alone, while 352 were unmedicated. Our meta-analysis evaluated 34 cognitive studies (N = 22,231) and 60 neuroimaging studies: 30 of T2DM (N = 866) and 30 of aging (N = 1088). Compared to age, sex, education, and hypertension-matched HC, T2DM was associated with marked cognitive deficits, particularly in executive functioning and processing speed . Likewise, we found that the diagnosis of T2DM was significantly associated with gray matter atrophy, primarily within the ventral striatum , cerebellum , and putamen , with reorganization of brain activity (decreased in the caudate and premotor cortex and increased in the subgenual area , orbitofrontal cortex, brainstem, and posterior cingulate cortex ). The structural and functional changes associated with T2DM show marked overlap with the effects correlating with age but appear earlier, with disease duration linked to more severe neurodegeneration. Metformin treatment status was not associated with improved neurocognitive outcomes. Conclusions: The neurocognitive impact of T2DM suggests marked acceleration of normal brain aging. T2DM gray matter atrophy occurred approximately 26% ± 14% faster than seen with normal aging; disease duration was associated with increased neurodegeneration. Mechanistically, our results suggest a neurometabolic component to brain aging. Clinically, neuroimaging-based biomarkers may provide a valuable adjunctive measure of T2DM progression and treatment efficacy based on neurological effects. Funding: The research described in this article was funded by the W. M. Keck Foundation (to LRMP), the White House Brain Research Through Advancing Innovative Technologies (BRAIN) Initiative (NSFNCS-FR 1926781 to LRMP), and the Baszucki Brain Research Fund (to LRMP). None of the funding sources played any role in the design of the experiments, data collection, analysis, interpretation of the results, the decision to publish, or any aspect relevant to the study. DJW reports serving on data monitoring committees for Novo Nordisk. None of the authors received funding or in-kind support from pharmaceutical and/or other companies to write this article. 

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2. Machine learning-based approaches for identifying human blood cells harboring CRISPR-mediated fetal chromatin domain ablations

   https://doi.org/10.1038/s41598-022-05575-3  

   Li, Yi ; Zaheri, Shadi ; Nguyen, Khai ; Liu, Li ; Hassanipour, Fatemeh ; Pace, Betty S. ; Bleris, Leonidas ( January 2022 , Scientific Reports)

   Two common hemoglobinopathies, sickle cell disease (SCD) and β-thalassemia, arise from genetic mutations within the β-globin gene. In this work, we identified a 500-bp motif (Fetal Chromatin Domain, FCD) upstream of human ϒ-globin locus and showed that the removal of this motif using CRISPR technology reactivates the expression of ϒ-globin. Next, we present two different cell morphology-based machine learning approaches that can be used identify human blood cells (KU-812) that harbor CRISPR-mediated FCD genetic modifications. Three candidate models from the first approach, which uses multilayer perceptron algorithm (MLP 20-26, MLP26-18, and MLP 30-26) and flow cytometry-derived cellular data, yielded 0.83 precision, 0.80 recall, 0.82 accuracy, and 0.90 area under the ROC (receiver operating characteristic) curve when predicting the edited cells. In comparison, the candidate model from the second approach, which uses deep learning (T2D5) and DIC microscopy-derived imaging data, performed with less accuracy (0.80) and ROC AUC (0.87). We envision that equivalent machine learning-based models can complement currently available genotyping protocols for specific genetic modifications which result in morphological changes in human cells.

    

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3. Embedding properties of network realizations of dissipative reduced order models

   Druskin, Guddati ( July 2022 , HOUSEHOLDER SYMPOSIUM XXI)

   Embedding properties of network realizations of dissipative reduced order models Jörn Zimmerling, Mikhail Zaslavsky,Rob Remis, Shasri Moskow, Alexander Mamonov, Murthy Guddati, Vladimir Druskin, and Liliana Borcea Mathematical Sciences Department, Worcester Polytechnic Institute https://www.wpi.edu/people/vdruskin Abstract Realizations of reduced order models of passive SISO or MIMO LTI problems can be transformed to tridiagonal and block-tridiagonal forms, respectively, via dierent modications of the Lanczos algorithm. Generally, such realizations can be interpreted as ladder resistor-capacitor-inductor (RCL) networks. They gave rise to network syntheses in the rst half of the 20th century that was at the base of modern electronics design and consecutively to MOR that tremendously impacted many areas of engineering (electrical, mechanical, aerospace, etc.) by enabling ecient compression of the underlining dynamical systems. In his seminal 1950s works Krein realized that in addition to their compressing properties, network realizations can be used to embed the data back into the state space of the underlying continuum problems. In more recent works of the authors Krein's ideas gave rise to so-called nite-dierence Gaussian quadrature rules (FDGQR), allowing to approximately map the ROM state-space representation to its full order continuum counterpart on a judicially chosen grid. Thus, the state variables can be accessed directly from the transfer function without solving the full problem and even explicit knowledge of the PDE coecients in the interior, i.e., the FDGQR directly learns" the problem from its transfer function. This embedding property found applications in PDE solvers, inverse problems and unsupervised machine learning. Here we show a generalization of this approach to dissipative PDE problems, e.g., electromagnetic and acoustic wave propagation in lossy dispersive media. Potential applications include solution of inverse scattering problems in dispersive media, such as seismic exploration, radars and sonars. To x the idea, we consider a passive irreducible SISO ROM fn(s) = Xn j=1 yi s + σj , (62) assuming that all complex terms in (62) come in conjugate pairs. We will seek ladder realization of (62) as rjuj + vj − vj−1 = −shˆjuj , uj+1 − uj + ˆrj vj = −shj vj , (63) for j = 0, . . . , n with boundary conditions un+1 = 0, v1 = −1, and 4n real parameters hi, hˆi, ri and rˆi, i = 1, . . . , n, that can be considered, respectively, as the equivalent discrete inductances, capacitors and also primary and dual conductors. Alternatively, they can be viewed as respectively masses, spring stiness, primary and dual dampers of a mechanical string. Reordering variables would bring (63) into tridiagonal form, so from the spectral measure given by (62 ) the coecients of (63) can be obtained via a non-symmetric Lanczos algorithm written in J-symmetric form and fn(s) can be equivalently computed as fn(s) = u1. The cases considered in the original FDGQR correspond to either (i) real y, θ or (ii) real y and imaginary θ. Both cases are covered by the Stieltjes theorem, that yields in case (i) real positive h, hˆ and trivial r, rˆ, and in case (ii) real positive h,r and trivial hˆ,rˆ. This result allowed us a simple interpretation of (62) as the staggered nite-dierence approximation of the underlying PDE problem [2]. For PDEs in more than one variables (including topologically rich data-manifolds), a nite-dierence interpretation is obtained via a MIMO extensions in block form, e.g., [4, 3]. The main diculty of extending this approach to general passive problems is that the Stieltjes theory is no longer applicable. Moreover, the tridiagonal realization of a passive ROM transfer function (62) via the ladder network (63) cannot always be obtained in port-Hamiltonian form, i.e., the equivalent primary and dual conductors may change sign [1]. 100 Embedding of the Stieltjes problems, e.g., the case (i) was done by mapping h and hˆ into values of acoustic (or electromagnetic) impedance at grid cells, that required a special coordinate stretching (known as travel time coordinate transform) for continuous problems. Likewise, to circumvent possible non-positivity of conductors for the non-Stieltjes case, we introduce an additional complex s-dependent coordinate stretching, vanishing as s → ∞ [1]. This stretching applied in the discrete setting induces a diagonal factorization, removes oscillating coecients, and leads to an accurate embedding for moderate variations of the coecients of the continuum problems, i.e., it maps discrete coecients onto the values of their continuum counterparts. Not only does this embedding yields an approximate linear algebraic algorithm for the solution of the inverse problems for dissipative PDEs, it also leads to new insight into the properties of their ROM realizations. We will also discuss another approach to embedding, based on Krein-Nudelman theory [5], that results in special data-driven adaptive grids. References [1] Borcea, Liliana and Druskin, Vladimir and Zimmerling, Jörn, A reduced order model approach to inverse scattering in lossy layered media, Journal of Scientic Computing, V. 89, N1, pp. 136,2021 [2] Druskin, Vladimir and Knizhnerman, Leonid, Gaussian spectral rules for the three-point second dierences: I. A two-point positive denite problem in a semi-innite domain, SIAM Journal on Numerical Analysis, V. 37, N 2, pp.403422, 1999 [3] Druskin, Vladimir and Mamonov, Alexander V and Zaslavsky, Mikhail, Distance preserving model order reduction of graph-Laplacians and cluster analysis, Druskin, Vladimir and Mamonov, Alexander V and Zaslavsky, Mikhail, Journal of Scientic Computing, V. 90, N 1, pp 130, 2022 [4] Druskin, Vladimir and Moskow, Shari and Zaslavsky, Mikhail LippmannSchwingerLanczos algorithm for inverse scattering problems, Inverse Problems, V. 37, N. 7, 2021, [5] Mark Adolfovich Nudelman The Krein String and Characteristic Functions of Maximal Dissipative Operators, Journal of Mathematical Sciences, 2004, V 124, pp 49184934 Go back to Plenary Speakers Go back to Speakers Go back 

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4. Content Sharing Design for Social Welfare in Networked Disclosure Game

   Jia, Feiran ; Qiu, Chenxi ; Rajtmajer, Sarah ; Squicciarini, Anna ( July 2023 , In Uncertainty in Artificial Intelligence, Proceedings of Machine Learning Research)

   This work models the costs and benefits of per- sonal information sharing, or self-disclosure, in online social networks as a networked disclosure game. In a networked population where edges rep- resent visibility amongst users, we assume a leader can influence network structure through content promotion, and we seek to optimize social wel- fare through network design. Our approach con- siders user interaction non-homogeneously, where pairwise engagement amongst users can involve or not involve sharing personal information. We prove that this problem is NP-hard. As a solution, we develop a Mixed-integer Linear Programming algorithm, which can achieve an exact solution, and also develop a time-efficient heuristic algo- rithm that can be used at scale. We conduct nu- merical experiments to demonstrate the properties of the algorithms and map theoretical results to a dataset of posts and comments in 2020 and 2021 in a COVID-related Subreddit community where privacy risks and sharing tradeoffs were particularly pronounced. 

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5. Seasonal iron fluxes and iron cycling in sandy bioirrigated sediments

   https://doi.org/10.3389/fmars.2023.1293893  

   Swenson Perger, Darci A. ; Dwyer, Ian P. ; Aller, Robert C. ; Volkenborn, Nils ; Heilbrun, Christina ; Wehrmann, Laura M. ( November 2023 , Frontiers in Marine Science)

   Permeable sediments, which represent more than 50% of the continental shelves, have been largely neglected as a potential source of Fe in current global estimates of benthic dissolved iron Fed fluxes. There are open questions regarding the effects of a range of factors on Fed fluxes from these deposits, including seasonal dynamics and the role of bioirrigation. To address these gaps, we performed laboratory-based sediment incubation experiments with muddy sands during summer (21 °C) and winter (7 °C). We used bioirrigation mimics to inject overlying water into the permeable sediment with patterns resembling the bioirrigation activity of the prolific bioturbating polychaete,Clymenella torquata. Newly developed in-line Fe accumulators were used to estimate Fe fluxes with a recirculating set-up. We found high Fed fluxes from sandy sediments, especially in benthic chambers with simulated bioirrigation. In the winter fluxes reached 200 µmol Fed m-2 d-1 at the onset of irrigation and then decreased over the course of a 13-day experiment while in the summer fluxes from irrigated sediments reached 100 µmol Fed m-2 d-1 and remained high throughout a 7-day experiment. Despite different geochemical expressions of Fe-S cycling and resulting porewater Fed concentrations in winter and summer, large Fed fluxes were sustained during both seasons. Solid-phase and porewater concentration profiles showed that maximum concentrations of key constituents, including total solid-phase reactive Fe, and porewater Fed and ammonium, were located closer to the sediment water interface (SWI) in irrigated cores than in non-irrigated cores due to the upward advective transport of dissolved porewater constituents. This upward transport also facilitated Fed fluxes out of the sediments, especially during times of active pumping. Our study demonstrates the potential for large Fed fluxes from sandy sediments in both summer and winter, despite relatively low standing stocks of labile organic matter and porewater Fed. The primary driver of these high fluxes was advective porewater transport, in our study induced by the activity of infaunal organisms. These results suggest that permeable sediments, which dominate shelf regions, must be explicitly considered in global estimates of benthic Fed fluxes, and cannot be simply extrapolated from estimates based on muddy sediments. 

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