Learning spatio-temporal patterns with Neural Cellular Automata

Neural Cellular Automata (NCA) are a powerful combination of machine learning and mechanistic modelling. We train NCA to learn complex dynamics from time series of images and PDE trajectories. Our method is designed to identify underlying local rules that govern large scale dynamic emergent behaviours. Previous work on NCA focuses on learning rules that give stationary emergent structures. We extend NCA to capture both transient and stable structures within the same system, as well as learning rules that capture the dynamics of Turing pattern formation in nonlinear Partial Differential Equations (PDEs). We demonstrate that NCA can generalise very well beyond their PDE training data, we show how to constrain NCA to respect given symmetries, and we explore the effects of associated hyperparameters on model performance and stability. Being able to learn arbitrary dynamics gives NCA great potential as a data driven modelling framework, especially for modelling biological pattern formation.Comment: For videos referenced in appendix, see: https://github.com/AlexDR1998/NCA/tree/main/Video

NPR1 Protein Regulates Pathogenic and Symbiotic Interactions between Rhizobium and Legumes and Non-Legumes

BACKGROUND:Legumes are unique in their ability to establish symbiotic interaction with rhizobacteria from Rhizobium genus, which provide them with available nitrogen. Nodulation factors (NFs) produced by Rhizobium initiate legume root hair deformation and curling that entrap the bacteria, and allow it to grow inside the plant. In contrast, legumes and non-legumes activate defense responses when inoculated with pathogenic bacteria. One major defense pathway is mediated by salicylic acid (SA). SA is sensed and transduced to downstream defense components by a redox-regulated protein called NPR1. METHODOLOGY/PRINCIPAL FINDINGS:We used Arabidopsis mutants in SA defense pathway to test the role of NPR1 in symbiotic interactions. Inoculation of Sinorhizobium meliloti or purified NF on Medicago truncatula or nim1/npr1 A. thaliana mutants induced root hair deformation and transcription of early and late nodulins. Application of S. meliloti or NF on M. truncatula or A. thaliana roots also induced a strong oxidative burst that lasted much longer than in plants inoculated with pathogenic or mutualistic bacteria. Transient overexpression of NPR1 in M. truncatula suppressed root hair curling, while inhibition of NPR1 expression by RNAi accelerated curling. CONCLUSIONS/SIGNIFICANCE:We show that, while NPR1 has a positive effect on pathogen resistance, it has a negative effect on symbiotic interactions, by inhibiting root hair deformation and nodulin expression. Our results also show that basic plant responses to Rhizobium inoculation are conserved in legumes and non-legumes

An MBR Membrane Housing Design Sustainable Treatment of Domestic Wastewater

ME450 Capstone Design and Manufacturing Experience: Winter 2008Anaerobic membrane housing design for use in wastewater treatment.Professor Lutgarde Raskin Mrs. Tanna Borrellhttp://deepblue.lib.umich.edu/bitstream/2027.42/58674/1/me450w08project27_report.pd

Pharmacological and genetic manipulations of Ca2+ signaling have contrasting effects on auxin-regulated trafficking

A large part of a plants’ developmental plasticity relies on the activities of the phytohormone auxin and the regulation of its own distribution. This process involves a cohort of transcriptional and non-transcriptional effects of auxin on polar auxin transport, regulating the abundancy, biochemical activity and polar localization of the molecular components, predominantly PIN auxin exporters. While the transcriptional auxin signaling cascade has been well characterized, the mechanism and role of non-transcriptional auxin signaling remains largely elusive. Here, we addressed the potential involvement of auxin-induced Ca2+ signaling in auxin’s inhibitory effect on PIN endocytic trafficking. On the one hand, exogenous manipulations of Ca2+ availability and signaling effectively antagonized auxin effects suggesting that auxin-induced Ca2+ signaling is required for inhibition of internalization. On the other hand, we addressed the auxin-mediated inhibition of PIN internalization in the auxin signaling (tir1afb2,3) or Ca2+ channel (cngc14) mutants. These mutants were strongly defective in auxin-triggered Ca2+ signaling, but not in auxin-inhibited internalization. These data imply that, while Ca2+ signaling may be required for normal PIN trafficking, auxin-mediated increase in Ca2+ signaling is not a direct part of a downstream mechanism that mediates auxin effects on Brefeldin A-visualized PIN intercellular aggregation. These contrasting results obtained by comparing the mutant analysis versus the exogenous manipulations of Ca2+ availability and signaling illustrate the critical importance of genetics to unravel the role of Ca2+ in a process of interest

The Vehicle, Fall 2002

Table of Contents Caterpillar DreamsAubrey Bonannopage 4 GrandmotherNatalie Espositopage 5 PhotographNatalie Espositopage 5 For My SisterAnn Hudsonpage 6 BuckeyeCaleb Judypage 6 A Moment\u27s GlowMelissa Knoblockpage 7 April 8,1994Andy Kochpage 8 Koch FuneralsAndy Kochpage 9 Grandpa Koch\u27s Sense of HumorAndy Kochpage 10 DeparturesDave Moutraypage 11 1958 VetteAlex Nicolpage 11 HomelandDave Moutraypage 12 The TravelerDave Moutraypage 12 GrandpaJennifer Probstpage 13 Confusion upon LearningJody Sanchezpage 14 Chucktown PrideMike Scalespage 14 I Might be WrongDallas Schumacherpage 15-20 UntitledAlex Nicholpage 21 Late NightRachel Seftonpage 22 Old DreamsRachel Seftonpage 23 Two-Minded ThoughtsRachel Sefton & Jodi Sanchezpage 24 Strange GraffitiMike Scalespage 24 On PoetryNick Slicerpage 25-26 Sometimes Things Just Happen That WayThomas Webbpage 26-33 Biographiespage 34-35 Editor\u27s Notepage 36https://thekeep.eiu.edu/vehicle/1076/thumbnail.jp

Ground and Aerial Robots for Agricultural Production: Opportunities and Challenges

Crop and animal production techniques have changed significantly over the last century. In the early 1900s, animal power was replaced by tractor power that resulted in tremendous improvements in field productivity, which subsequently laid foundation for mechanized agriculture. While precision agriculture has enabled site-specific management of crop inputs for improved yields and quality, precision livestock farming has boosted efficiencies in animal and dairy industries. By 2020, highly automated systems are employed in crop and animal agriculture to increase input efficiency and agricultural output with reduced adverse impact on the environment. Ground and aerial robots combined with artificial intelligence (AI) techniques have potential to tackle the rising food, fiber, and fuel demands of the rapidly growing population that is slated to be around 10 billion by the year 2050. This Issue Paper presents opportunities provided by ground and aerial robots for improved crop and animal production, and the challenges that could potentially limit their progress and adoption. A summary of enabling factors that could drive the deployment and adoption of robots in agriculture is also presented along with some insights into the training needs of the workforce who will be involved in the next-generation agriculture

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

Structural and biochemical characterization of the KLHL3-WNK kinase interaction important in blood pressure regulation

WNK1 [with no lysine (K)] and WNK4 regulate blood pressure by controlling the activity of ion co-transporters in the kidney. Groundbreaking work has revealed that the ubiquitylation and hence levels of WNK isoforms are controlled by a Cullin-RING E3 ubiquitin ligase complex (CRL3KLHL3) that utilizes CUL3 (Cullin3) and its substrate adaptor, KLHL3 (Kelch-like protein 3). Loss-of-function mutations in either CUL3 or KLHL3 cause the hereditary high blood pressure disease Gordon's syndrome by stabilizing WNK isoforms. KLHL3 binds to a highly conserved degron motif located within the C-terminal non-catalytic domain of WNK isoforms. This interaction is essential for ubiquitylation by CRL3KLHL3 and disease-causing mutations in WNK4 and KLHL3 exert their effects on blood pressure by disrupting this interaction. In the present study, we report on the crystal structure of the KLHL3 Kelch domain in complex with the WNK4 degron motif. This reveals an intricate web of interactions between conserved residues on the surface of the Kelch domain β-propeller and the WNK4 degron motif. Importantly, many of the disease-causing mutations inhibit binding by disrupting critical interface contacts. We also present the structure of the WNK4 degron motif in complex with KLHL2 that has also been reported to bind WNK4. This confirms that KLHL2 interacts with WNK kinases in a similar manner to KLHL3, but strikingly different to how another KLHL protein, KEAP1 (Kelch-like enoyl-CoA hydratase-associated protein 1), binds to its substrate NRF2 (nuclear factor-erythroid 2-related factor 2). The present study provides further insights into how Kelch-like adaptor proteins recognize their substrates and provides a structural basis for how mutations in WNK4 and KLHL3 lead to hypertension