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At least 109 records · Page 6

Rendering the Topological Spines

Many tools to analyze and represent high dimensional data already exits yet most of them are not flexible, informative and intuitive enough to help the scientists make the corresponding analysis and predictions, understand the structure and complexity of scientific data, get a complete picture of it and explore a greater number of hypotheses. With this in mind, N-Dimensional Data Analysis and Visualization (ND²AV) is being developed to serve as an interactive visual analysis platform with the purpose of coupling together a number of these existing tools that range from statistics, machine learning, and data mining, with new techniques, in particular with new visualization approaches. My task is to create the rendering and implementation of a new concept called topological spines in order to extend ND²AV's scope. Other existing visualization tools create a representation preserving either the topological properties or the structural (geometric) ones because it is challenging to preserve them both simultaneously. Overcoming such challenge by creating a balance in between them, the topological spines are introduced as a new approach that aims to preserve them both. Its render using OpenGL and C++ and is currently being tested to further on be implemented on ND²AV. In this paper I will present what are the Topological Spines and how they are rendered.

97 MATHEMATICS AND COMPUTING↗

PIPER: Performance Insights for Programmers and Exascale Runtimes

During the lifetime of the project, the PIPER at the University of Utah worked in collaboration with the team from the partner institutions to establish a set of software tools for analyzing and improving the performance parallel computing tools. These activities complement and complete the work performed by the other X-Stack 2 projects with the definition of a common data models and computing infrastructures, which have been a central element in the targeted performance analysis pipeline and new programming models. The University of Utah team have focused mainly on developing data analysis and visualization systems to facilitate exploration, comparison and evaluation of the behavior and performance of complex algorithms in modern HPC infrastructures. This is involved several demonstrations of the performance achieved and presentation of the results in a way that facilitates the users understand bottlenecks and ways to overcome them. One major focus of the University of Utah activities has been the analysis of the performance characteristics of Fat-Tree and Dragonfly topology networks. The work involved the development of practical visualization systems especially in collaboration with the team at LLNL, and published several papers and gave invited talks at prestigious venues such as the Salishan Conference on High-Speed Computing or the International Conference on High Performance Computing, Data, and Analytics. In addition, the university of Utah team has advanced the core activities on analyzing the performance characteristics of I/O and other data movement systems and their practical use for scaling Uintah and other simulation codes poised for use in the exascale computing environments of the future.

42 ENGINEERING↗

Systems Life Cycle and Its Relation with the Triple Helix

This chapter examines the life cycle of complex systems in light of the dynamic interconnections among the university, industry and government sectors. Each sector is motivated in its resource allocation by principles discussed elsewhere in this book and yet remains complementary es-tablishing enduring and fundamental relationships. Industry and Government depend upon an educated workforce; universities depend upon industry to spark the R&D which is needed and to sponsor some basic research and much applied research. Government depends upon industry to address operational needs and provide finished products while universities offer government (along with industry) problem solving and problem solving environments. The life cycle of complex systems in this chapter will be examined in this context, providing historical examples. Current examples will then be examined within this multi-dimensional context with respect to the phases of program and project life cycle management from requirements definition through retirement and closeout of systems. During the explanation of these examples, the advances in research techniques to collect, analyze, and process the data will be examined.

and Law↗

Nationwide Buildings Energy Research enabled through an integrated Data Intensive Scientific Workflow and Advanced Analysis Environment

Modern workflow systems enable scientists to run ensemble simulations at unprecedented scales and levels of complexity, allowing them to study system sizes previously impossible to achieve, due to the inherent resource requirements needed for the modeling work. However as a result of these new capabilities the science teams suddenly also face unprecedented data volumes that they are unable to analyze with their existing tools and methodologies in a timely fashion. In this paper we will describe the ongoing development work to create an integrated data intensive scientific workflow and analysis environment that offers researchers the ability to easily create and execute complex simulation studies and provides them with different scalable methods to analyze the resulting data volumes. The integration of simulation and analysis environments is hereby not only a question of ease of use, but supports fundamental functions in the correlated analysis of simulation input, execution details and derived results for multi-variant, complex studies. To this end the team extended and integrated the existing capabilities of the Velo data management and analysis infrastructure, the MeDICi data intensive workflow system and RHIPE the R for Hadoop version of the well-known statistics package, as well as developing a new visual analytics interface for the result exploitation by multi-domain users. The capabilities of the new environment are demonstrated on a use case that focusses on the Pacific Northwest National Laboratory (PNNL) building energy team, showing how they were able to take their previously local scale simulations to a nationwide level by utilizing data intensive computing techniques not only for their modeling work, but also for the subsequent analysis of their modeling results. As part of the PNNL research initiative PRIMA (Platform for Regional Integrated Modeling and Analysis) the team performed an initial 3 year study of building energy demands for the US Eastern Interconnect domain, which they are now planning to extend to predict the demand for the complete century. The initial study raised their data demands from a few GBs to 400GB for the 3year study and expected tens of TBs for the full century.

99 GENERAL AND MISCELLANEOUS↗

Loop dynamics of thymidine diphosphate-rhamnose 3'-O-methyltransferase (CalS11), an enzyme in calicheamicin biosynthesis

Structure analysis and ensemble refinement of the apo-structure of thymidine diphosphate (TDP)-rhamnose 3'-O-methyltransferase reveal a gate for substrate entry and product release. TDP-rhamnose 3'-O-methyltransferase (CalS11) catalyses a 3'-O-methylation of TDP-rhamnose, an intermediate in the biosynthesis of enediyne antitumor antibiotic calicheamicin. CalS11 operates at the sugar nucleotide stage prior to glycosylation step. Here, we present the crystal structure of the apo form of CalS11 at 1.89 Å resolution. We propose that the L2 loop functions as a gate facilitating and/or providing specificity for substrate entry or promoting product release. Ensemble refinement analysis slightly improves the crystallographic refinement statistics and furthermore provides a compelling way to visualize the dynamic model of loop L2, supporting the understanding of its proposed role in catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Workflow for Visual Diagnostics of Binary Classifiers using Instance-Level Explanations

In this paper, we propose a visual analytics workflow to help data scientists explore, diagnose, and understand the decisions made by a binary classifier. The approach leverages “instance-level explanations”, measures of local feature relevance that explain single instances and uses them to build a set of visual representations that guide the users in their investigation. The workflow is based on three main visual representations and steps: one based on aggregate statistics to see how data distributes across correct or incorrect decisions; one based on explanations to understand which features are used to make these decisions; and one based on raw data, to derive insights on potential root causes for the observed patterns. The work is validated through a long-term collaboration with a group of healthcare professionals who used our method to make sense of machine learning models they developed. The case studies from this collaboration demonstrate that the proposed method helps experts derive useful knowledge about the model and the phenomena it describes and also generates useful hypotheses on how a model can be improved.

Krause, Josua↗

Tracing Interstellar Magnetic Field Using Velocity Gradient Technique: Application to Atomic Hydrogen Data

The advancement of our understanding of MHD turbulence opens ways to develop new techniques to probe magnetic fields. In MHD turbulence, the velocity gradients are expected to be perpendicular to magnetic fields and this fact was used by González-Casanova and Lazarian to introduce a new technique to trace magnetic fields using velocity centroid gradients (VCGs). The latter can be obtained from spectroscopic observations. We apply the technique to GALFA-H i survey data and then compare the directions of magnetic fields obtained with our technique to the direction of magnetic fields obtained using PLANCK polarization. We find an excellent correspondence between the two ways of magnetic field tracing, which is obvious via the visual comparison and through the measuring of the statistics of magnetic field fluctuations obtained with the polarization data and our technique. This suggests that the VCGs have a potential for measuring of the foreground magnetic field fluctuations, and thus provide a new way of separating foreground and CMB polarization signals.

79 ASTRONOMY AND ASTROPHYSICS↗

Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction

Understanding dynamics in complex systems is challenging because there are many degrees of freedom, and those that are most important for describing events of interest are often not obvious. The leading eigenfunctions of the transition operator are useful for visualization, and they can provide an efficient basis for computing statistics, such as the likelihood and average time of events (predictions). Here, we develop inexact iterative linear algebra methods for computing these eigenfunctions (spectral estimation) and making predictions from a dataset of short trajectories sampled at finite intervals. We demonstrate the methods on a low-dimensional model that facilitates visualization and a high-dimensional model of a biomolecular system. Implications for the prediction problem in reinforcement learning are discussed.

Chemistry↗

Enhancements to VTK enabling Scientific Visualization in Immersive Environments

Modern scientific, engineering and medical computational sim- ulations, as well as experimental and observational data sens- ing/measuring devices, produce enormous amounts of data. While statistical analysis provides insight into this data, scientific vi- sualization is tactically important for scientific discovery, prod- uct design and data analysis. These benefits are impeded, how- ever, when scientific visualization algorithms are implemented from scratch—a time-consuming and redundant process in im- mersive application development. This process can greatly ben- efit from leveraging the state-of-the-art open-source Visualization Toolkit (VTK) and its community. Over the past two (almost three) decades, integrating VTK with a virtual reality (VR) environment has only been attempted to varying degrees of success. In this pa- per, we demonstrate two new approaches to simplify this amalga- mation of an immersive interface with visualization rendering from VTK. In addition, we cover several enhancements to VTK that pro- vide near real-time updates and efficient interaction. Finally, we demonstrate the combination of VTK with both Vrui and OpenVR immersive environments in example applications.

97 MATHEMATICS AND COMPUTING↗

Changing-look Active Galactic Nuclei from the Dark Energy Spectroscopic Instrument. II. Statistical Properties from the First Data Release

We present the identification of changing-look active galactic nuclei (CL-AGNs) from the Dark Energy Spectroscopic Instrument First Data Release and Sloan Digital Sky Survey Data Release 16 at z ≤ 0.9. To confirm the CL-AGNs, we utilize spectral flux calibration assessment via an [O III ]-based calibration, pseudophotometry examination, and visual inspection. This rigorous selection process allows us to compile a statistical catalog of 561 CL-AGNs, encompassing 527 Hβ, 149 Hα, and 129 Mg II CL behaviors. In this sample, we find (1) a 283:278 ratio of turn-on to turn-off CL-AGNs. (2) The median Eddington ratio for CL-AGNs in the dim state is approximately λ Edd ∼ 0.01. (3) A strong correlation between the change in the luminosity of the broad emission lines (BELs) and variation in the continuum luminosity, with Mg II and Hβ displaying similar responses during CL phases. (4) The Baldwin–Phillips–Terlevich diagram for CL-AGNs shows no statistical difference from the general AGN catalog. (5) Five CL-AGNs are associated with asymmetrical mid-infrared flares, possibly linked to tidal disruption events. Given the large CL-AGN sample and the stochastic sampling of spectra, we propose that some CL phenomena are inherently due to typical AGN variability during low accretion rates, particularly for CL phenomenon only occurring on one BEL. Finally, we introduce a monotonically dimming CL phase for objects characterized by a gradual decline over decades in the light curve and the complete disappearance of entire BELs in faint spectra, indicative of a real transition in the accretion disk.

accretion↗

Changing-look Active Galactic Nuclei from the Dark Energy Spectroscopic Instrument. II. Statistical Properties from the First Data Release

We present the identification of changing-look active galactic nuclei (CL-AGNs) from the Dark Energy Spectroscopic Instrument First Data Release and Sloan Digital Sky Survey Data Release 16 at z≤ 0.9. To confirm the CL-AGNs, we utilize spectral flux calibration assessment via an [O iii]-based calibration, pseudophotometry examination, and visual inspection. This rigorous selection process allows us to compile a statistical catalog of 561 CL-AGNs, encompassing 527 Hβ, 149 Hα, and 129 Mg ii CL behaviors. In this sample, we find (1) a 283:278 ratio of turn-on to turn-off CL-AGNs. (2) The median Eddington ratio for CL-AGNs in the dim state is approximately λ$_{Edd}$ ∼ 0.01. (3) A strong correlation between the change in the luminosity of the broad emission lines (BELs) and variation in the continuum luminosity, with Mg ii and Hβ displaying similar responses during CL phases. (4) The Baldwin–Phillips–Terlevich diagram for CL-AGNs shows no statistical difference from the general AGN catalog. (5) Five CL-AGNs are associated with asymmetrical mid-infrared flares, possibly linked to tidal disruption events. Given the large CL-AGN sample and the stochastic sampling of spectra, we propose that some CL phenomena are inherently due to typical AGN variability during low accretion rates, particularly for CL phenomenon only occurring on one BEL. Finally, we introduce a monotonically dimming CL phase for objects characterized by a gradual decline over decades in the light curve and the complete disappearance of entire BELs in faint spectra, indicative of a real transition in the accretion disk.

79 ASTRONOMY AND ASTROPHYSICS↗

PET optimization for improved assessment and accurate quantification of {sup 90}Y-microsphere biodistribution after radioembolization

Purpose: {sup 90}Y-microspheres are widely used for the radioembolization of metastatic liver cancer or hepatocellular carcinoma and there is a growing interest for imaging {sup 90}Y-microspheres with PET. The aim of this study is to evaluate the performance of a current generation PET/CT scanner for {sup 90}Y imaging and to optimize the PET protocol to improve the assessment and the quantification of {sup 90}Y-microsphere biodistribution after radioembolization. Methods: Data were acquired on a Biograph mCT-TrueV scanner with time of flight (TOF) and point spread function (PSF) modeling. Spatial resolution was measured with a{sup 90}Y point source. Sensitivity was evaluated using the NEMA 70 cm line source filled with {sup 90}Y. To evaluate the count rate performance, {sup 90}Y vials with activity ranging from 3.64 to 0.035 GBq were measured in the center of the field of view (CFOV). The energy spectrum was evaluated. Image quality with different reconstructions was studied using the Jaszczak phantom containing six hollow spheres (diameters: 31.3, 28.1, 21.8, 16.1, 13.3, and 10.5 mm), filled with a 207 kBq/ml {sup 90}Y concentration and a 5:1 sphere-to-background ratio. Acquisition time was adjusted to simulate the quality of a realistic clinical PET acquisition of a patient treated with SIR-Spheres{sup ®}. The developed methodology was applied to ten patients after SIR-Spheres{sup ®} treatment acquiring a 10 min per bed PET. Results: The energy spectrum showed the{sup 90}Y bremsstrahlung radiation. The {sup 90}Y transverse resolution, with filtered backprojection reconstruction, was 4.5 mm in the CFOV and degraded to 5.0 mm at 10 cm off-axis. {sup 90}Y absolute sensitivity was 0.40 kcps/MBq in the center of the field of view. Tendency of true and random rates as a function of the {sup 90}Y activity could be accurately described using linear and quadratic models, respectively. Phantom studies demonstrated that, due to low count statistics in {sup 90}Y PET acquisition, the optimal parameters for the standard OSEM+PSF reconstruction were only one iteration and a postreconstruction filter of 6 mm FWHM, for both TOF and non-TOF reconstructions. Moreover, when TOF is included, the signal to noise ratio increased and visibility achieved 100% by the experienced observers and 93.3% according to the Rose model of statistical detection. In 50% of patients, TOF allowed the visualization of {sup 90}Y radioembolized lesions not seen without TOF, confirming phantom results. Liver activity was accurately quantified, with no significant differences between reconstructed and actual delivered activity to the whole-liver [mean relative difference (10.2 ± 14.7)%]. Conclusions: Qualitative and quantitative{sup 90}Y PET imaging improved with the introduction of TOF in a PET/CT scanner, thereby allowing the visualization of microsphere deposition in lesions not visible in non-TOF images. This technique accurately quantifies the total activity delivered to the liver during radioembolization with {sup 90}Y-microspheres and allows dose estimation.

60 APPLIED LIFE SCIENCES↗

Clinical evaluation of a medical high dynamic range display

Purpose: Recent new medical displays do have higher contrast and higher luminance but do not have a High Dynamic Range (HDR). HDR implies a minimum luminance value close to zero. A medical HDR display prototype based on two Liquid Crystal layers has been developed. The goal of this study is to evaluate the potential clinical benefit of such display in comparison with a low dynamic range (LDR) display. Methods: The study evaluated the clinical performance of the displays in a search and detection task. Eight radiologists read chest x-ray images some of which contained simulated lung nodules. The study used a JAFROC (Jacknife Free Receiver Operating Characteristic) approach for analyzing FROC data. The calculated figure of merit (FoM) is the probability that a lesion is rated higher than all rated nonlesions on all images. Time per case and accuracy for locating the center of the nodules were also compared. The nodules were simulated using Samei’s model. 214 CR and DR images [half were “healthy images” (chest nodule-free) and half “diseased images”] were used resulting in a total number of nodules equal to 199 with 25 images with 1 nodule, 51 images with 2 nodules, and 24 images with 3 nodules. A dedicated software interface was designed for visualizing the images for each session. For the JAFROC1 statistical analysis, the study is done per nodule category: all nodules, difficult nodules, and very difficult nodules. Results: For all nodules, the averaged FoM{sub HDR} is slightly higher than FoM{sub LDR} with 0.09% of difference. For the difficult nodules, the averaged FoM{sub HDR} is slightly higher than FoM{sub LDR} with 1.38% of difference. The averaged FoM{sub HDR} is slightly higher than FoM{sub LDR} with 0.71% of difference. For the true positive fraction (TPF), both displays (the HDR and the LDR ones) have similar TPF for all nodules, but looking at difficult and very difficult nodules, there are more TP for the HDR display. The true positive fraction has been also computed in function of the local average luminance around the nodules. For the lowest luminance range, there is more than 30% in favor of the HDR display. For the highest luminance range, there is less than 6% in favor of the LDR display. Conclusions: This study shows the potential benefit of using a HDR display in radiology.

60 APPLIED LIFE SCIENCES↗

Turbulent Processes that Influence Boundary-Layer Cloud Structure (Final Technical Report)

Many models of the atmosphere simulate vertical profiles of observable fields, such as temperature, moisture, and vertical velocity. To assess the realism of such model output, it is important to evaluate the modeled profiles against observations. However, many extant evaluations consist of comparing time averaged profiles from the model and the observations. Such time averages can smooth out unrealistic features that appear in instantaneous profiles. In this way, the time averages may obscure certain model errors from detection. For instance, many models misrepresent turbulent processes, leading to profiles that are too smoothed out or too noisy. E.g., if a model has coarse vertical resolution and overly strong diffusion, then the model may be unable to produce observed sharp peaks. On the other hand, a model may have artificial approximations that produce spurious jumps in the vertical. Much can be learned by browsing through instantaneous snapshots of model output. But the volume of output produced by a global model is far too great to rely purely on visual inspection. In addition, we need a way to statistically characterize the profiles, so that anomalies can be detected more conveniently.

54 ENVIRONMENTAL SCIENCES↗

ILLICIT TRANSIT INTERDICTION GLOBAL ANALYSIS

This study aims to enhance the security of radioactive materials during transport by analyzing commonalities in cargo thefts conducted by non-state groups such as thieves and terrorists. This research focuses on identifying patterns and trends in the methods used to steal high-value cargo, with the goal of applying these insights to improve transport security of radioactive materials. Key questions addressed include the frequency of specific tools, techniques, and insider involvement in thefts, as well as the use of weapons, electronic jamming equipment, and specialized tools. Findings will inform security design improvements and industry practices to mitigate vulnerabilities. The study involves a comprehensive review of literature and case studies, utilizing data sources from 2018 to 2023. Articles will be selected based on their relevance to thefts of valuable cargo in transit, with a focus on incidents involving non-state actors. The methodology will include statistical and inferential analysis to identify trends, with results visualized through pie charts, frequency analyses, and terrain maps. The discussion will highlight the implications of findings and provide actionable recommendations for strengthening security measures. Limitations such as data availability and reporting inconsistencies will be acknowledged. Suggestions for future improvements will be constructed using existing case studies and expert feedback. The study’s outcomes aim to raise awareness within the industry, inform policy decisions, and enhance security protocols for radioactive material transport. Metrics for impact include the potential publication of findings, presentations at conferences to raise awareness, and the subsequent actions taken by stakeholders based on the research. By identifying trends and vulnerabilities and suggesting improvements, this research contributes to preventing the illicit use of nuclear and radiological materials.

Zineddin, Dr. Z. [ORNL] (ORCID:0009000848740725)↗

Λ Baryon Production in ν¯µ Interactions in the MicroBooNE Detector

The Cabibbo suppressed production of $\Lambda$ baryons in anti-neutrino interactions with nuclei is a rare process that is yet to be measured with a modern neutrino detector with automated reconstruction. The cross section for this process is sensitive to a number of unique nuclear effects, most notably the secondary interactions of the produced hyperon while attempting to escape from the nucleus. Other interactions within the nuclear remnant can impact the estimation of neutrino energy in oscillation measurements, and thus an accurate description of the nuclear environment is required. The strangeness violating hyperon production process is only available to anti-neutrinos. The model of this interaction is implemented into the NuWro neutrino interaction Monte Carlo simulation, and some predictions are presented, focusing on the role of nuclear effects. This model introduces a hyperon-nucleus potential, which calculations from hypernuclear theory permit to be strongly repulsive in th e case of $\Sigma$ baryons. The presence of this potential is found to sculpt the shape of the differential cross section in some variables. The MicroBooNE detector will be described, followed by a description of a measurement of the flux averaged, restricted phase space cross section of Cabibbo suppressed $\Lambda$ baryon production. A sophisticated event selection is employed, as a very large quantity of background neutrino interactions must be removed to perform the measurement with any sensitivity. This selection introduces some novel techniques such as the island finding method, and achieves a background reduction of $\sim 10^6$, with an efficiency of around 7\%. The calculation of the systematic uncertainties will be explained, including two procedures explored to handle sources of background with extremely poor simulation statistics: an in-situ constraint using data from sidebands, and a visual inspection of the data and simulation to remove the troublesome background events. The sensitivity to the $\Lambda$ baryon production cross section is calculated in the form of Bayesian posterior probability distributions, combining the systematic uncertainties with data and simulation statistical uncertainties. As a rare process, the statistical uncertainties are highly non-Gaussian, and the Bayesian approach is applied to include the full shapes of these uncertainties. Data corresponding to $2.2 \times 10^{20}$ protons on target of neutrino mode running and $4.9 \times 10^{20}$ protons on target of anti-neutrino running is analysed. When the data was unblinded, five $\Lambda$ production candidates were selected from the data, consistent with the MC simulation prediction of $5.3 \pm 1.1$ events. The final estimated cross section is $1.8^{+2.0}_{-1.6} \times 10^{-40}$cm$^2/$Ar when employing the sideband constraint procedure. A similar result of $2.0^{+2.2}_{-1.8} \times 10^{-40}$cm$^2/$Ar is obtained when performing the visual scan instead. The methods used in t his analysis are intended to be easily exported to other LArTPC detectors such as the Short Baseline Near Detector.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Adaptive Performance-Constrained in Situ Visualization of Atmospheic Simulations

While many parallel visualization tools now provide in situ visualization capabilities, the trend has been to feed such tools with large amounts of unprocessed output data and let them render everything at the highest possible resolution. This leads to an increased run time of simulations that still have to complete within a fixed-length job allocation. In this paper, we tackle the challenge of enabling in situ visualization under performance constraints. Our approach shuffles data across processes according to its content and filters out part of it in order to feed a visualization pipeline with only a reorganized subset of the data produced by the simulation. Our framework leverages fast, generic evaluation procedures to score blocks of data, using information theory, statistics, and linear algebra. It monitors its own performance and adapts dynamically to achieve appropriate visual fidelity within predefined performance constraints. Experiments on the Blue Waters supercomputer with the CM1 simulation show that our approach enables a 5 speedup with respect to the initial visualization pipeline and is able to meet performance constraints.

54 ENVIRONMENTAL SCIENCES↗

Experimental study of crystallization fouling by calcium carbonate: Effects of surface structure and material

We report mitigation of crystallization fouling on heat transfer surface is crucial for developing highly efficient desalination techniques, because the tenacious and porous crystal layer can drastically deteriorate system efficiency. Surface modification is a potential approach to decrease scale formation and promote crystal removal, but some of the mechanisms between crystallization and substrate properties are still not fully understood. In this study, we use dual-angle microscopic visualization and image processing to quantify three-dimensional crystallization behavior and analyze the impact of surface structure and material. The transition of crystal size and distance with roughness and wettability are identified from statistical analysis. The determination of crystal porosity and effective thermal conductivity is enabled by visualized geometry and measured deposition mass. This study shed lights on potential strategies of surface modification to mitigate scaling in desalination by enhancing scale removal and localizing crystal growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗