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At least 901 records · Page 50

New insights into the natural history of bronchopulmonary dysplasia from proteomics and multiplexed immunohistochemistry

Bronchopulmonary dysplasia (BPD) is a disease of prematurity related to the arrest of normal lung development. The objective of this study was to better understand how proteome modulation and cell-type shifts are noted in BPD pathology. Pediatric human donors aged 1–3 yr were classified based on history of prematurity and histopathology consistent with “healed” BPD (hBPD, n = 3) and “established” BPD (eBPD, n = 3) compared with respective full-term born (n = 6) age-matched term controls. Proteins were quantified by tandem mass spectroscopy with selected Western blot validations. Multiplexed immunofluorescence (MxIF) microscopy was performed on lung sections to enumerate cell types. Protein abundances and MxIF cell frequencies were compared among groups using ANOVA. Cell type and ontology enrichment were performed using an in-house tool and/or EnrichR. Proteomics detected 5,746 unique proteins, 186 upregulated and 534 downregulated, in eBPD versus control with fewer proteins differentially abundant in hBPD as compared with age-matched term controls. Cell-type enrichment suggested a loss of alveolar type I, alveolar type II, endothelial/capillary, and lymphatics, and an increase in smooth muscle and fibroblasts consistent with MxIF. Histochemistry and Western analysis also supported predictions of upregulated ferroptosis in eBPD versus control. Finally, several extracellular matrix components mapping to angiogenesis signaling pathways were altered in eBPD. Despite clear parsing by protein abundance, comparative MxIF analysis confirms phenotypic variability in BPD. This work provides the first demonstration of tandem mass spectrometry and multiplexed molecular analysis of human lung tissue for critical elucidation of BPD trajectory-defining factors into early childhood.

60 APPLIED LIFE SCIENCES↗

Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions in Synechococcus elongatus PCC 7942 despite limited accuracy in predicting direct regulator-gene interactions

Synechococcus elongatus PCC 7942 is a model organism for studying circadian regulation and bioproduction, where precise temporal control of metabolism significantly impacts photosynthetic efficiency and CO 2 -to-bioproduct conversion. Despite extensive research on core clock components, our understanding of the broader regulatory network orchestrating genome-wide metabolic transitions remains incomplete. We address this gap by applying machine learning tools and network analysis to investigate the transcriptional architecture governing circadian-controlled gene expression. While our approach showed moderate accuracy in predicting individual transcription factor-gene interactions - a common challenge with real expression data - network-level topological analysis successfully revealed the organizational principles of circadian regulation. Our analysis identified distinct regulatory modules coordinating day-night metabolic transitions, with photosynthesis and carbon/nitrogen metabolism controlled by day-phase regulators, while nighttime modules orchestrate glycogen mobilization and redox metabolism. Through network centrality analysis, we identified potentially significant but previously understudied transcriptional regulators: HimA as a putative DNA architecture regulator, and TetR and SrrB as potential coordinators of nighttime metabolism, working alongside established global regulators RpaA and RpaB. This work demonstrates how network-level analysis can extract biologically meaningful insights despite limitations in predicting direct regulatory interactions. The regulatory principles uncovered here advance our understanding of how cyanobacteria coordinate complex metabolic transitions and may inform metabolic engineering strategies for enhanced photosynthetic bioproduction from CO 2 .

59 BASIC BIOLOGICAL SCIENCES↗

Energy and mobility impacts of connected autonomous vehicles with co-optimization of speed and powertrain on mixed vehicle platoons

Intersections are known to be traffic bottlenecks where a significant amount of energy consumption could be caused due to deceleration/acceleration in the presence of red signals. With an increased level of connectivity and automation of intelligent transportation systems, connected autonomous vehicles (CAVs) are expected to be able to proactively adjust their driving strategies subject to constraints imposed by the predicted future traffic. As a result, many potential benefits can be achieved, such as improved energy efficiency, enhanced traffic safety, among many others. Notably, the way CAVs are controlled affects the following legacy vehicles (LVs) due to complex traffic dynamics. Here, we are particularly interested in studying the energy and mobility impact of CAVs with an improved traffic prediction method on mixed vehicle platoons at various market penetration rates. Leveraging traffic prediction, CAVs are controlled with co-optimization of their speed and gear position. Specifically, a traffic prediction framework in a rolling horizon fashion is employed based upon a modified Payne–Whitham (PW) model capable of handling mixed traffic consisting of CAVs and LVs. The prediction error of the modified PW model is reduced by 53.62% compared to that of the standard PW model under test scenarios. According to the predicted traffic conditions, speed and gear position of CAVs are co-optimized with the primary goal of minimizing energy consumption when driving on a signalized arterial. The energy benefits achieved by CAVs and the impact of CAVs on LVs behind are studied comprehensively for mixed vehicle platoons. The lead LV follows a real-world speed profile collected on TH-55 in Minnesota. Numerical results show that energy benefits achieved by the vehicle platoon range from 2% to 16%, and a 1% to 5% reduction in travel time for LVs behind CAVs is also observed, at different penetration rates of CAVs in various traffic scenarios. Furthermore, it is observed that CAVs using the proposed eco-driving approach appear to have a positive impact on the LVs behind in terms of energy consumption, regardless of the driving styles of the LVs ahead.

33 ADVANCED PROPULSION SYSTEMS↗

Vector-level feedforward control of LPBF melt pool area using a physics-based thermal model

Laser powder bed fusion (LPBF) is an additive manufacturing technique that has gained popularity thanks to its ability to produce geometrically complex, fully dense metal parts. However, these parts are prone to internal defects and geometric inaccuracies, stemming in part from variations in the melt pool. Here, this paper proposes a novel vector-level feedforward control framework for regulating melt pool area in LPBF. By decoupling part-scale thermal behavior from small-scale melt pool physics, the controller provides a scale-agnostic prediction of melt pool area and efficient optimization over it. This is done by operating on two coupled lightweight models: a finite-difference thermal model that efficiently captures vector-level temperature fields and a reduced-order, analytical melt pool model. Each model is calibrated separately with minimal single-track and 2D experiments, and the framework is validated on a complex 3D geometry in both Inconel 718 and 316L stainless steel. Results showed that feedforward vector-level laser power scheduling reduced geometric inaccuracy in key dimensions by 62%, overall porosity by 16.5%, and photodiode root-mean-squared deviation by 38.5% on average. Overall, this modular, data-efficient approach demonstrates that proactively compensating for known thermal effects can significantly improve part quality while remaining computationally efficient and readily extensible to other materials and machines.

Additive manufacturing↗

Quantifying wildfire drivers and predictability in boreal peatlands using a two-step error-correcting machine learning framework in TeFire v1.0

Abstract. Wildfires are becoming an increasing challenge to the sustainability of boreal peatland (BP) ecosystems and can alter the stability of boreal carbon storage. However, predicting the occurrence of rare and extreme BP fires proves to be challenging, and gaining a quantitative understanding of the factors, both natural and anthropogenic, inducing BP fires remains elusive. Here, we quantified the predictability of BP fires and their primary controlling factors from 1997 to 2015 using a two-step correcting machine learning (ML) framework that combines multiple ML classifiers, regression models, and an error-correcting technique. We found that (1) the adopted oversampling algorithm effectively addressed the unbalanced data and improved the recall rate by 26.88 %–48.62 % when using multiple datasets, and the error-correcting technique tackled the overestimation of fire sizes during fire seasons; (2) nonparametric models outperformed parametric models in predicting fire occurrences, and the random forest machine learning model performed the best, with the area under the receiver operating characteristic curve ranging from 0.83 to 0.93 across multiple fire datasets; and (3) four sets of factor-control simulations consistently indicated the dominant role of temperature, air dryness, and climate extreme (i.e., frost) for boreal peatland fires, overriding the effects of precipitation, wind speed, and human activities. Our findings demonstrate the efficiency and accuracy of ML techniques in predicting rare and extreme fire events and disentangle the primary factors determining BP fires, which are critical for predicting future fire risks under climate change.

54 ENVIRONMENTAL SCIENCES↗

Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography

Abstract Wetlands store 20–30% of the world’s soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.

Environmental Sciences & Ecology↗

Predictive turbulence-driven flux model of scrape-off layer widths across confinement regimes in tokamaks

Reliable scrape-off layer (SOL) profile decay lengths predictions are needed to design and operate future tokamaks. The present manuscript describes a new model based on turbulent transport that is able to predict SOL widths for both L-mode and H-mode plasmas. The model is based upon the sheared-spectral filament paradigm (Peret et al (WEST Team) 2022 Phys. Plasmas 29 072306), however, incorporating the effects of thermal transport in order to calculate the parallel heat fluxes. The effects of magnetic shear and ExB shear on the cross-field transport are crucial to explain the shorter SOL decay lengths found in H-mode. The model is validated against a database of thousands of DIII-D L-mode and H-mode SOL profiles. We also calculate SOL decay length predictions in terms of plasma and engineer control parameters, which are in agreement with the multi-machine empirical H-mode scaling (Eich et al (ASDEX Upgrade Team and JET EFDA Contributors) 2013 Nucl. Fusion 53 093031), however, with an additional device geometry dependence. ITER SOL width predictions by the model are 3 times higher than the empirical scaling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Energy transfer between localized emitters in photonic cavities from first principles

Radiative and nonradiative resonant couplings between defects are ubiquitous phenomena in photonic devices used in classical and quantum information technology applications. In this work, we present a first-principles approach to enable quantitative predictions of the energy transfer between defects in photonic cavities, beyond the dipole-dipole approximation and including the many-body nature of the electronic states. As an example, we discuss the energy transfer from a dipolelike emitter to an 𝐹 center in MgO in a spherical cavity. We show that the cavity can be used to controllably enhance or suppress specific spin-flip and spin-conserving transitions. Specifically, we predict that an ∼10–100 enhancement in the resonant energy transfer rate can be gained in the case of the 𝐹 center in MgO at ∼10 nm distances from a dipolar source, using rather moderate cavity with quality factor 𝑄 ∼ 400. We also show that a similar suppression in the transfer rate can be achieved by off-tuning the cavity resonance relative to the emitter transition energy. The framework presented here is general and readily applicable to a wide range of devices where localized emitters are embedded in microspheres, core-shell nanoparticles, and dielectric Mie resonators. Hence, our approach paves the way to predict how to control energy transfer in quantum memories and in ultrahigh-density optical memories, and in a variety of quantum information platforms.

First-principles calculations↗

Probabilistic error estimation for non-intrusive reduced models learned from data of systems governed by linear parabolic partial differential equations

This work derives a residual-based a posteriori error estimator for reduced models learned with non-intrusive model reduction from data of high-dimensional systems governed by linear parabolic partial differential equations with control inputs. It is shown that quantities that are necessary for the error estimator can be either obtained exactly as the solutions of least-squares problems in a non-intrusive way from data such as initial conditions, control inputs, and high-dimensional solution trajectories or bounded in a probabilistic sense. Here, the computational procedure follows an offline/online decomposition. In the offline (training) phase, the high-dimensional system is judiciously solved in a black-box fashion to generate data and to set up the error estimator. In the online phase, the estimator is used to bound the error of the reduced-model predictions for new initial conditions and new control inputs without recourse to the high-dimensional system. Numerical results demonstrate the workflow of the proposed approach from data to reduced models to certified predictions.

97 MATHEMATICS AND COMPUTING↗

Aligning theoretical and empirical representations of soil carbon-to-nitrogen stoichiometry with process-based terrestrial biogeochemistry models

Soil carbon-nitrogen (C:N) stoichiometry acts as a control over decomposition and soil organic matter formation and loss, making it a key soil property for understanding ecosystem dynamics and projected ecosystems responses to global environmental change. However, the controls of soil C:N and how they respond to increasing pressures from global change agents are not fully understood. The “foundational” controls on soil C:N, namely plant and microbial C:N, have been used to predict soil C:N, but fail to accurately simulate all ecosystems and may be insufficient for predictions under global environmental change. Here we present an “emerging” representation of controls of soil C:N that includes plant-microbe-mineral feedbacks that have been shown to regulate soil C:N. We argue that including representation of these emerging drivers in process-based terrestrial biogeochemistry models, which include biological N fixation, mycorrhizae, priming, root exudation of organic acids, and mineralogy (including soil texture, mineral composition, and aggregation), will improve mechanistic representation of soil C:N and associated processes. Such improvements will produce models that will better simulate a variety of ecological states and predict soil C:N when global changes modify plant-microbe-mineral interactions. Here, we align our empirical understanding of controls of soil C:N with those controls represented in models, identifying contexts where emerging drivers might be particularly important to represent (e.g., priming and root exudation in nutrient-limited conditions) and areas of future work. Additionally, we show that implementing emerging drivers of soil C:N results in different simulated outcomes at steady state and in response to elevated atmospheric CO2. Our review and preliminary simulations support the need to incorporate emerging drivers of soil C:N into process-based terrestrial biogeochemistry models, allowing for both theoretical exploration of mechanisms and potentially more accurate predictions of land biogeochemical responses to global change.

54 ENVIRONMENTAL SCIENCES↗

Point defect energetics in gallium arsenide, a comprehensive density functional theory study

In materials, point defects often control or modify functional properties. To predict the performance of materials intended for application in optoelectronic devices, it is imperative to understand the properties of those point defects. For the first time, all six intrinsic defects of GaAs, a key optoelectronics material, and their charge transition levels are calculated using density functional theory with the HSE06 functional. For comparison, both PBE and r 2 SCAN calculations are also carried out. The HSE06 results are found to be in better agreement with experimental data than previous calculations. In conclusion, the importance of using the exact electron exchange present in hybrid functionals and larger supercells to accurately determine defect levels and ground state defect configurations is demonstrated.

36 MATERIALS SCIENCE↗

A Lens into the Cu Nanograin by In Situ Vibrational Spectroscopy

Cu-based catalysts are uniquely capable of C-C coupling during electrochemical CO 2 reduction (CO 2 R), yet further mechanistic understanding remains hampered by the lack of spectroscopically resolved descriptors that demonstrate how surface adsorbates emerge and evolve within their catalytic environment. Here, in this study, we correlate in situ surface-enhanced Raman spectroscopy (SERS) and surface-enhanced infrared absorption spectroscopy (SEIRAS) to resolve the potential-dependent dynamics during CO 2 R on Cu nanograin catalysts. By building on previous benchmarking of low overpotential performance and nanograin structural evolution, we offer a diagnostic framework linking vibrational signatures to catalytic function, unveiling which species appear, persist, and turnover as the electrified surface and interfacial environment evolve under bias. The onset of linear CO is marked below -0.45 V, coincident with persistent adsorbed *OH/*O domains beyond the CO 2 R onset. In this context, Cu nanograins serve as a platform to dissect contributions of adsorbate coverage. By carefully dissecting the potential dependence of emergent twin-defect/step CO stretch bands (P1-P2), alongside the prototypical terrace-site CO stretch band (P3), we provide important context for interpreting coupled spectroscopic trends driven by coverage effects and resolve this for the evidently complex nanograin morphology. Together, these observations highlight the intertwined roles of surface stabilization and interfacial flux in steering multicarbon product formation. By directly linking vibrational signatures to catalytic behavior, this work aims to bridge the gap between observation and control and help guide toward a predictive framework of fine-tuned selectivity for CO 2 R.

Fonseca Guzman, Maria V. [University of California↗

Observation of magnetic islands in tokamak plasmas during the suppression of edge-localized modes

In tokamaks, a leading platform for fusion energy, periodic filamentary plasma eruptions known as edge-localized modes occur in plasmas with high-energy confinement and steep pressure profiles at the plasma edge. These edge-localized modes could damage the tokamak wall but can be suppressed using small three-dimensional magnetic perturbations. Here we demonstrate that these magnetic perturbations can change the magnetic topology just inside the steep gradient region of the plasma edge. We identify signatures of a magnetic island, and their observation is linked to the suppression of edge-localized modes. We compare high-resolution measurements of perturbed magnetic surfaces with predictions from ideal magnetohydrodynamic theory where the magnetic topology is preserved. Although ideal magnetohydrodynamics adequately describes the measurements in plasmas exhibiting edge-localized modes, it proves insufficient for plasmas where these modes are suppressed. Nonlinear resistive magnetohydrodynamic modelling supports this observation. Our study experimentally confirms the predicted role of magnetic islands in inhibiting the occurrence of edge-localized modes. This will be beneficial for physics-based predictions in future fusion devices to control these modes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Experimental evidence for recovery of mercury-contaminated fish populations

Anthropogenic releases of mercury (Hg) are a human health issue because the potent toxicant methylmercury (MeHg), formed primarily by microbial methylation of inorganic Hg in aquatic ecosystems, bioaccumulates to high concentrations in fish consumed by humans. Predicting the efficacy of Hg pollution controls on fish MeHg concentrations is complex because many factors influence the production and bioaccumulation of MeHg. Here we conducted a 15-year whole-ecosystem, single-factor experiment to determine the magnitude and timing of reductions in fish MeHg concentrations following reductions in Hg additions to a boreal lake and its watershed. During the seven-year addition phase, we applied enriched Hg isotopes to increase local Hg wet deposition rates fivefold. The Hg isotopes became increasingly incorporated into the food web as MeHg, predominantly from additions to the lake because most of those in the watershed remained there. Thereafter, isotopic additions were stopped, resulting in an approximately 100% reduction in Hg loading to the lake. The concentration of labelled MeHg quickly decreased by up to 91% in lower trophic level organisms, initiating rapid decreases of 38–76% of MeHg concentration in large-bodied fish populations in eight years. Although Hg loading from watersheds may not decline in step with lowering deposition rates, this experiment clearly demonstrates that any reduction in Hg loadings to lakes, whether from direct deposition or runoff, will have immediate benefits to fish consumers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predicting microstructurally sensitive fatigue‐crack path in WE43 magnesium using high‐fidelity numerical modeling and three‐dimensional experimental characterization

Abstract Microstructurally small fatigue‐crack growth in polycrystalline materials is highly three‐dimensional due to sensitivity to local microstructural features (e.g., grains). One requirement for modeling microstructurally sensitive crack propagation is establishing the criteria that govern crack evolution, including crack deflection. Here, a high‐fidelity finite‐element modeling framework is used to assess the performance and validity of various crack‐growth criteria, including slip‐based metrics (e.g., fatigue‐indicator parameters), as potential criteria for predicting three‐dimensional crack paths in polycrystalline materials. The modeling framework represents cracks as geometrically explicit discontinuities and involves voxel‐based remeshing, mesh‐gradation control, and a crystal‐plasticity constitutive model. The predictions are compared to experimental measurements of WE43 magnesium samples subject to fatigue loading, for which three‐dimensional grain structures and fatigue‐crack surfaces were measured post‐mortem using near‐field high‐energy x‐ray diffraction microscopy and x‐ray computed tomography. Findings from this work are expected to improve the predictive capabilities of simulations involving microstructurally small fatigue‐crack growth in polycrystalline materials.

Engineering↗

A review on the application of machine learning for combustion in power generation applications

Abstract Although the world is shifting toward using more renewable energy resources, combustion systems will still play an important role in the immediate future of global energy. To follow a sustainable path to the future and reduce global warming impacts, it is important to improve the efficiency and performance of combustion processes and minimize their emissions. Machine learning techniques are a cost-effective solution for improving the sustainability of combustion systems through modeling, prediction, forecasting, optimization, fault detection, and control of processes. The objective of this study is to provide a review and discussion regarding the current state of research on the applications of machine learning techniques in different combustion processes related to power generation. Depending on the type of combustion process, the applications of machine learning techniques are categorized into three main groups: (1) coal and natural gas power plants, (2) biomass combustion, and (3) carbon capture systems. This study discusses the potential benefits and challenges of machine learning in the combustion area and provides some research directions for future studies. Overall, the conducted review demonstrates that machine learning techniques can play a substantial role to shift combustion systems towards lower emission processes with improved operational flexibility and reduced operating cost.

Engineering↗

Ply Strength Prediction of Unidirectional Continuous Carbon Fiber Composites

As inhomogeneous orthotropic materials, composite mechanical properties can be difficult to predict. Even with tight fabrication process controls, there is always some microstructural variation that will affect these properties. As a highly defect-dependent phenomena, mechanical strength is even more subject to variation, especially considering that composites exhibit multiple potential failure modes. The most direct way to determine composite material strength is via experimental testing, maintaining loading and specimen morphology as close as possible to the in situ states. When multiple materials and designs are being considered, this process is often prohibitively costly and slow. However, some approximations and rules of thumb can consistently guide the design process and consideration of alternatives.

36 MATERIALS SCIENCE↗

Investigation of design principles for metal-binding and conductive protein assemblies

Throughout the lifetime of this initiative, including renewals, we focused on understanding the fundamental principles of protein-protein interface design that enable predictable and modular spatial and kinetic control of multi-component protein self-assembly in 1D, 2D, and 3D, including the interface with inorganic materials, small molecules, and metal ions. We designed individual protein components that bind specific metal ions, including REEs and transport ions across lipid membranes. We created helical 1D filaments of repeating units with programmed periodicity, pitch, and multi-component environmentally responsive self-assembling protein fibers. We showed that these filaments reversibly assemble and disassemble under specific pH conditions and created end-specific caps that independently tune the balance of attachment and detachment rates at each terminus of the filament. Using similar filaments, we succeeded in binding arrays of heme and chlorophyll molecules and assembling patterned helical coatings around carbon nanotubes in efforts to create de novo conductive nanowires. By arraying REE binding sites in a large circular tandem array with a repeat protein-based cyclic oligomer, we created a molecular scaffold for superradiance and paramagnetic quantum sensing. We created a range of one-component and two-component self-assembling 2D arrays and showed that when designed to engage cell receptors, these arrays can control cell behavior from outside the cell signal to inside the cell. We designed helical repeat proteins with variable lengths displaying charged residues in a pattern matched to the cation lattice of mica. achieved a range of ordered states with an epitaxial match to the underlying crystal lattice. We further applied the learned principles of protein-induced biomineralization to design proteins with an interface lattice matching CaCO 3 and guide the formation of specific crystal forms of CaCO 3 from solution, a significant advance toward the global need to manage carbon. In all cases of mineral lattice matching and biomineralization, we followed assembly using molecularly resolved in situ AFM imaging and extracted information about assembly pathways and energetics, applying deep learning to quantify the dynamics of protein self-organization. We developed techniques for using dynamic metal-dependent interfaces on protein nanopores for discriminatively sensing dilute REEs in solution and demonstrated the use of strong metal-binding interfaces to drive nanocage disassembly for conditional nanocompartmentalization applications. This grant supported 11 people, including Asim Bera, Evans Brackenbrough, Andrew Borst, Nikita Hanikel, Timothy Huddy, Emily Joyce, Alex Young-Seug Kang, Ryan Kibler, Joshua Morris Lubner, Harley Pyles, and Shuai Zhang. The research effort culminated in the production of published papers and theses. Electronic Thesis/Dissertation are distributed by ProQuest/UMI Dissertation Publishing and made available on an open access basis through UW Libraries ResearchWorks Service.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗