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At least 721 records · Page 40

Image registration of low signal-to-noise cryo-STEM data

Combining multiple fast image acquisitions to mitigate scan noise and drift artifacts has proven essential for picometer precision, quantitative analysis of atomic resolution scanning transmission electron microscopy (STEM) data. For very low signal-to-noise ratio (SNR) image stacks – frequently required for undistorted imaging at liq- uid nitrogen temperatures – image registration is particularly delicate, and standard approaches may either fail, or produce subtly specious reconstructed lattice images. We present an approach which effectively registers and averages image stacks which are challenging due to their low-SNR and propensity for unit cell misalignments. Registering all possible image pairs in a multi-image stack leads to significant information surplus. In combination with a simple physical picture of stage drift, this enables identi cation of incorrect image registrations, and determination of the optimal image shifts from the complete set of relative shifts. Here, we demonstrate the effectiveness of our approach on experimental, cryogenic STEM datasets, highlighting subtle artifacts endemic to low-SNR lattice images and how they can be avoided. High-SNR average images with information transfer out to 0.72 Å are achieved at 300 kV and with the sample cooled to near liquid nitrogen temperature.

47 OTHER INSTRUMENTATION↗

Toward accurate measurement of electromagnetic field by retrieving and refining the center position of non-uniform diffraction disks in Lorentz 4D-STEM

Recent advancement in scanning transmission electron microscopy (STEM) allows the use of 4D-STEM, a technique that captures an electron diffraction pattern at each scan point in STEM, to measure electrostatic and magnetic potential and field in materials. However, accurate measurement, separation of the magnetic and electric signals, and removal of artifacts remain challenging, especially in the presence of complex non-uniform diffraction contrast within the disks. In this work, based on dynamic simulations of 4D-STEM patterns built upon superstructures consisting of millions of atoms to account for different sample thickness and edge geometries, we show how the shape and intensity distribution of the central disk are affected by multiple scattering. We propose a robust refinement procedure through iteration of the spin-sensitive peak position of the disk-center in the circular Hough transform filtered images from experimental Lorentz 4D-STEM dataset after minimizing the possible artifacts, such as those due to the change of thickness, dynamic scattering, and scanning process. We verify that caution must be taken as in practice the rigid-disk-shift model used to reconstruct induction maps can easily break down due to disk-protrusion when there exists a nonconstant phase gradient or thickness within the width of the probe. Through quantitative analysis and comparing experiment with calculation the effect of the non-spin-related intensity distribution inside the disk as well as that causes the disk shift due to the intensity-protrusion can be removed, and high-quality magnetic field mapping is possible.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Bridging cognitive gaps between user and model in interactive dimension reduction

Interactive machine learning (ML) systems are difficult to design because of the "Two Black Boxes" problem that exists at the interface between human and machine. Many algorithms that are used in interactive ML systems are black boxes that are presented to users, while the human cognition represents a second black box that can be difficult for the algorithm to interpret. These two black boxes create cognitive gaps between the user and the interactive ML model when a user interacts with the system. In this paper, we identify several cognitive gaps that exist in a previously-developed interactive visual analytics (VA) system, Andromeda. These cognitive gaps that we are addressing in Andromeda are representative of common problems in other VA systems. Our goal with this work is to open both black boxes and bridge these cognitive gaps by making improvements to the original Andromeda system, including designing new visual features to help people better understand how Andromeda processes and interacts with data and improving the underlying algorithm so that the Andromeda system can better understand the intent of the user during the data exploration process. We evaluate our designs through both qualitative and quantitative analysis (i.e., user study and simulation analysis), and the results confirm that the improved Andromeda system outperforms the original version significantly in a series of high-dimensional data understanding tasks.

97 MATHEMATICS AND COMPUTING↗

Techno-economic assessment of emerging CO 2 electrolysis technologies

Recycling of waste CO 2 to bulk chemicals has a tremendous potential for the decarbonization of the chemical industry. Quantitative analysis of the prospects of this technology is hindered by the lack of flexible techno-economic assessment (TEA) models that enable evaluation of the processing costs under different deployment scenarios. In this protocol, we explain how to convert literature data into metrics useful for evaluation of the emerging electrolysis technologies, derive TEA models, and illustrate their use with a CO 2 -to-ethylene example. For complete details on the use and execution of this protocol, please refer to Barecka et al. (2021a).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The effects of chemical fixation on the cellular nanostructure

Chemical fixation is nearly indispensable in the biological sciences, especially in circumstances where cryo-fixation is not applicable. While universally employed for the preservation of cell organization, chemical fixatives often introduce artifacts that can confound identification of true structures. Since biological research is increasingly probing ever-finer details of the cellular architecture, it is critical to understand the nanoscale transformation of the cellular organization due to fixation both systematically and quantitatively. In this work, we employed Partial Wave Spectroscopic (PWS) Microscopy, a nanoscale sensitive and label-free live cell spectroscopic-imaging technique, to analyze the effects of the fixation process through three commonly used fixation protocols for cells in vitro. In each method investigated, we detected dramatic difference in both nuclear and cytoplasmic nanoarchitecture between live and fixed states. But significantly, despite the alterations in cellular nanoscale organizations after chemical fixation, the population differences in chromatin structure (e.g. induced by a specific chemotherapeutic agent) remains. In conclusion, we demonstrated that the nanoscale cellular arrangement observed in fixed cells was fundamentally divorced from that in live cells, thus the quantitative analysis is only meaningful on the population level. This finding highlights the importance of live cell imaging techniques with nanoscale sensitivity or cryo-fixation in the interrogation of cellular structure, to complement more traditional chemical fixation methods. - Highlights: • PWS was employed to monitor fixation process for the same cells in vitro. • Dramatic changes in cellular nanostructure were observed after fixation. • However, the population difference of chromatin structure remains after fixation.

60 APPLIED LIFE SCIENCES↗

Combination therapy with lenvatinib and radiation significantly inhibits thyroid cancer growth by uptake of tyrosine kinase inhibitor

Highlights: • Lenvatinib combined with radiation significantly inhibits thyroid cancer growth. • Combined therapy induced apoptosis and G2/M phase cell cycle arrest. • Irradiation increased cellular uptake of lenvatinib into cancer cells. • Combined therapy suggests a new therapeutic strategy for advanced thyroid cancer. Although surgical treatment cures >90% of differentiated thyroid cancer (DTC) patients, the remaining patients, including advanced DTC cases, have poor clinical outcomes. These patients with inoperable disease have only two choices of radioactive iodine therapy and tyrosine kinase inhibitors such as lenvatinib, which have a high incidence of treatment-related adverse events and can only prolong progression free survival by approximately 5–15 months. In this study, we investigated the antitumor effects of combination therapy with lenvatinib and radiation (CTLR) for DTC. CTLR synergistically inhibited cell replication and colony formation in vitro and tumor growth in nude mice without apparent toxicities and suppressed the expression of proliferation marker (Ki-67). CTLR also induced apoptosis and G2/M phase cell cycle arrest. Moreover, quantitative analysis of the intracellular uptake of lenvatinib using liquid chromatography and mass spectrometry demonstrated that intracellular uptake of lenvatinib was significantly increased 48 h following irradiation. These data suggest that increased membrane permeability caused by irradiation increases the intracellular concentration of levatinib, contributing to the synergistic effect. This mechanism-based potential of combination therapy suggests a powerful new therapeutic strategy for advanced thyroid cancer with fewer side effects and might be a milestone for developing a regimen in clinical practice.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Extracellular IL-37 promotes osteogenic and odontogenic differentiation of human dental pulp stem cells via autophagy

The osteogenic and odontogenic differentiation of dental pulp stem cells (DPSCs) contribute to restoration and regeneration of dental tissue. Previous study indicated that interleukin-37 (IL-37) was an anti-inflammatory factor that affected other pro-inflammatory signals. The aim of this study was to explore the effects of IL-37 on the differentiation of DPSCs. DPSCs were cultured in growth medium with different concentrations of IL-37. We selected the optimal concentration for the following experiments by alkaline phosphatase (ALP) activity analysis, quantitative reverse-transcription polymerase chain reaction (qRT-PCR) and Western blot. Cell counting kit assay (CCK-8) and 5-Ethynyl-2-Deoxyuridine (EdU) assay were conducted to assess the effects of IL-37 on the proliferation of DPSCs. ALP activity assay and staining, alizarin red S (ARS) staining, qRT‐PCR, Western blot as well as immunofluorescence staining were conducted to assess differentiation ability of DPSCs. Western blot, immunofluorescence staining and transmission electron microscopy (TEM) were utilized to examine cell autophagy. Results showed that IL-37 enhanced the osteogenic and odontogenic differentiation ability of DPSCs with no significant influence on the proliferation of DPSCs. Autophagy in DPSCs was activated by IL-37. Activation of autophagy enhanced osteogenesis and odontogenesis of DPSCs, whereas inhibition of autophagy suppressed DPSCs osteogenic and odontogenic differentiation. In conclusion, IL-37 increased osteogenic and odontogenic differentiation via autophagy.

60 APPLIED LIFE SCIENCES↗

Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks

Fatty alcohols in the C12-C18 range are used in personal care products, lubricants, and potentially biofuels. These compounds can be produced from the fatty acid pathway by a fatty acid reductase (FAR), yet yields from the preferred industrial host Saccharomyces cerevisiae remain under 2% of the theoretical maximum from glucose. Here we improved titer and yield of fatty alcohols using an approach involving quantitative analysis of protein levels and metabolic flux, engineering enzyme level and localization, pull-push-block engineering of carbon flux, and cofactor balancing. We compared four heterologous FARs, finding highest activity and endoplasmic reticulum localization from a Mus musculus FAR. After screening an additional twenty-one single-gene edits, we identified increasing FAR expression; deleting competing reactions encoded by DGA1, HFD1, and ADH6; overexpressing a mutant acetyl-CoA carboxylase; limiting NADPH and carbon usage by the glutamate dehydrogenase encoded by GDH1; and overexpressing the Δ9-desaturase encoded by OLE1 as successful strategies to improve titer. Our final strain produced 1.2 g/L fatty alcohols in shake flasks, and 6.0 g/L in fed-batch fermentation, corresponding to ~ 20% of the maximum theoretical yield from glucose, the highest titers and yields reported to date in S. cerevisiae. We further demonstrate high-level production from lignocellulosic feedstocks derived from ionic-liquid treated switchgrass and sorghum, reaching 0.7 g/L in shake flasks. Together, our work represents progress towards efficient and renewable microbial production of fatty acid-derived products.

09 BIOMASS FUELS↗

Deuterated water as a substrate-agnostic isotope tracer for investigating reversibility and thermodynamics of reactions in central carbon metabolism

Stable isotope tracers are a powerful tool for the quantitative analysis of microbial metabolism, enabling pathway elucidation, metabolic flux quantification, and assessment of reaction and pathway thermodynamics. 13 C and 2 H metabolic flux analysis commonly relies on isotopically labeled carbon substrates, such as glucose. However, the use of 2 H-labeled nutrient substrates faces limitations due to their high cost and limited availability in comparison to 13 C-tracers. Furthermore, isotope tracer studies in industrially relevant bacteria that metabolize complex substrates such as cellulose, hemicellulose, or lignocellulosic biomass, are challenging given the difficulty in obtaining these as isotopically labeled substrates. In this study, we examine the potential of deuterated water ( 2 H 2 O) as an affordable, substrate-neutral isotope tracer for studying central carbon metabolism. We apply 2 H 2 O labeling to investigate the reversibility of glycolytic reactions across three industrially relevant bacterial species -C. thermocellum, Z. mobilis, and E. coli-harboring distinct glycolytic pathways with unique thermodynamics. We demonstrate that 2 H 2 O labeling recapitulates previous reversibility and thermodynamic findings obtained with established 13 C and 2 H labeled nutrient substrates. Furthermore, we exemplify the utility of this 2 H 2 O labeling approach by applying it to high-substrate C. thermocellum fermentations -a setting in which the use of conventional tracers is impractical-thereby identifying the glycolytic enzyme phosphofructokinase as a major bottleneck during high-substrate fermentations and unveiling critical insights that will steer future engineering efforts to enhance ethanol production in this cellulolytic organism. This study demonstrates the utility of deuterated water as a substrate-agnostic isotope tracer for examining flux and reversibility of central carbon metabolic reactions, which yields biological insights comparable to those obtained using costly 2 H-labeled nutrient substrates.

09 BIOMASS FUELS↗

A Simple Preparation Method for Full-Range Electron Tomography of Nanoparticles and Fine Powders

Abstract Electron tomography has become a valuable and widely used tool for studying the three-dimensional nanostructure of materials and biological specimens. However, the incomplete tilt range provided by conventional sample holders limits the fidelity and quantitative interpretability of tomographic images by leaving a “missing wedge” of unknown information in Fourier space. Imaging over a complete range of angles eliminates missing wedge artifacts and dramatically improves tomogram quality. Full-range tomography is usually accomplished using needle-shaped samples milled from bulk material with focused ion beams, but versatile specimen preparation methods for nanoparticles and other fine powders are lacking. In this work, we present a new preparation technique in which powder specimens are supported on carbon nanofibers that extend beyond the end of a tungsten needle. Using this approach, we produced tomograms of platinum fuel cell catalysts and gold-decorated strontium titanate photocatalyst specimens. Without the missing wedge, these tomograms are free from elongation artifacts, supporting straightforward automatic segmentation and quantitative analysis of key materials properties such as void size and connectivity, and surface area and curvature. This approach may be generalized to other samples that can be dispersed in liquids, such as biological structures, creating new opportunities for high-quality electron tomography across disciplines.

Materials Science↗

Rietveld Refinement for Macromolecular Powder Diffraction

Powder X-ray diffraction (PXRD) has been employed extensively for the structural characterization of materials, quantitative analysis of multicomponent mixtures, phase identification, texture, and microstructural analysis. At the heart of all those lies the Rietveld method, which has revolutionized the use of powder diffraction for materials studies. Initially applied to minerals and inorganics, the Rietveld method has progressively been used for more complex materials, for instance, zeolites and pharmaceuticals. A major advance of the method came some 20 years ago, when the first protein structure was successfully refined. Because of the sheer complexity of macromolecules, several new approaches and algorithms had to be pioneered or adapted from macromolecular single-crystal diffraction experiments, thus constituting macromolecular PXRD a quite unique field of study. This review aims to provide necessary elements of theory and application of structure solution and refinement via the Rietveld method for macromolecular PXRD data. Here, practical explanations and highlighted case studies are also presented.

36 MATERIALS SCIENCE↗

Short-Range Mechanisms in the Creation of a ZnO/InGaAs Interface

Here we perform quantitative analysis of the X-ray absorption data taken in situ during the earliest cycles of the ZnO atomic layer deposition on atomically flat InGaAs (001) surfaces. As deposition progresses, we observe a transition from an amorphous structure to a nanocrystalline one. The former retains much of the characteristics of a ZnO crystal in the Zn coordination shell, while the latter shows atomic ordering up to at least the third neighbor shell of Zn atoms, despite the absence of Bragg X-ray diffraction peaks. We show that the different chemical preparation of the substrate surface affects the ZnO local structure and that, counterintuitively, a stronger short-range order is obtained in the nanostructures characterized by lower local order at the interface. We propose a model that accounts for these findings.

36 MATERIALS SCIENCE↗

Resonant X-ray Diffraction Reveals the Location of Counterions in Doped Organic Mixed Ionic Conductors

Organic mixed ionic–electronic conductors (OMIECs) have the potential to enable diverse new technologies, ranging from novel in situ biosensors to flexible energy storage devices and neuromorphic computing platforms. However, their complex behavior in functional films involving electrolyte-induced swelling, ion ingress, and electrochemical doping inhibits rational material design. Of critical importance is an understanding of the specific location of the ions in the volumetrically doped material, yet this information is not readily available. Here, in this report, we present the use of grazing- incidence resonant X-ray diffraction (RXRD, also known as anomalous diffraction) at S and Cl K-edges to determine the structure of a doped, prototypical, semicrystalline polymer OMIEC based on oligo(ethylene glycol) substitution of regioregular polythiophene. The RXRD measurement provides two key insights. Quantitative analysis of the RXRD allows the determination of the position of the ion relative to the polymer backbone in the crystalline regions. We find that the anion is relatively distant from the backbone, nearer to the lamella mid-plane naively in conflict with expected Coulombic attraction between the ion and the doped polymer polaron. Comparison of RXRD to Cl – fluorescence (total Cl – ) allows determination of the relative order of doping between the crystalline and amorphous regions. We find preferential doping of the crystalline regions. Both insights, the preferential doping of crystals at low potential and the specific location of the counterion with respect to the polymer backbone, are critical to developing a microscopic understanding of transport in OMIECs.

36 MATERIALS SCIENCE↗

Facile Synthesis of Oxyhydrides by Reaction with NaBH 4 in an Open System

Oxyhydrides are an intriguing class of materials in which there is partial replacement of the oxide ion with hydride ions and oxygen vacancies. Conventional synthesis relies on vacuum sealed ampules, using long reaction times at high temperatures, limiting accessibility. Here, we demonstrate a rapid, ambient-pressure route to oxyhydride formation using NaBH 4 under flowing argon in just 1 h. This approach significantly lowers experimental barriers, enabling broader exploration of these materials. The maximum hydride incorporation, obtained using a reaction temperature of 400 °C, is given by the formula SrTiO 2.945 H 0.049 , where the hydride, oxygen vacancy, and unpaired electron concentrations are determined through thermogravimetric analysis, quantitative solid-state nuclear magnetic resonance (NMR) spectroscopy, and electron paramagnetic resonance (EPR) spectroscopy. Density functional theory simulations of the 1 H NMR shifts for candidate point defects support the assignment of the observed hydride peak, validating the efficacy of the synthetic approach. A combination of in situ and ex situ studies of the reaction pathway reveal that hydride incorporation into the perovskite occurs via direct solid-solid reaction, with higher reaction temperatures favoring NaBH 4 decomposition and H 2 (g) release over oxyhydride formation. The electronic defect structure established from the EPR and NMR studies indicate that, at ambient temperature, anion vacant sites are occupied by single electrons, whereas hydride sites do not trap electrons. As a result, this work establishes a scalable synthesis strategy and provides a computational-experimental framework for understanding defect chemistry in oxyhydrides, opening pathways for their integration into energy and electronic applications.

Anions↗

Quantifying Impacts of Biomass Pelletization on Fast Pyrolysis Using a Single-Particle Reactor, X-ray Computed Tomography, and Computational Modeling

The pore structure and density of lignocellulosic feedstocks dictate intraparticle transport phenomena and thereby play an important role in thermochemical conversion processes such as fast pyrolysis for biofuel and biochemical production. Variations in microstructure are inherent from different biomass species and can be introduced by preprocessing techniques such as cutting and pelletization. Morphological changes also occur during conversion and lead to vastly different pore structures and behavior during pyrolysis, which impact required conversion times and product distributions. The current work presents a comprehensive comparison of fast pyrolysis of neat and pelletized pine feedstocks, which includes single-particle experiments, modeling, and 3D imaging by X-ray computed tomography (XCT). The particle-scale model included anisotropic heat and mass transport in a shrinking particle with pyrolysis reactions based on the CRECK mechanism with boundary conditions informed by reactor-scale simulations of the single-particle reactor. The models were validated by measurements of the temperature and mass loss from single-particle pyrolysis experiments of neat and pelletized pine. Quantitative analysis of XCT geometries revealed that pyrolytic conversion yielded chars with increased porosity and permeability compared to the unpyrolyzed materials, along with decreased tortuosity and anisotropy. Pelletization of the pine feedstock resulted in a much denser, less permeable material, which converted slower and produced more residual char after pyrolysis compared to neat pine. The results from particle modeling revealed that accounting for the dynamic and anisotropic heat and mass transport caused by differences in pore structure is critical to achieving agreement with experimental results. Overall, this study highlights the dramatic differences in conversion behavior imparted by pelletization and the importance of capturing microstructural attributes in computational models to guide the design and optimization of pyrolysis processes for specific biomass feedstocks.

09 BIOMASS FUELS↗

Molecular Characterization of Water-Soluble Brown Carbon Chromophores in Snowpack from Northern Xinjiang, China

This study reports molecular-level characterization of brown carbon (BrC) attributed to water-soluble organic carbon in six snowpack samples collected from northern Xinjiang, China. Here, the molecular composition and light-absorbing properties of BrC chromophores were unraveled by application of high-performance liquid chromatography (HPLC) coupled to a photodiode array (PDA) detector and high-resolution mass spectrometry. The chromophores were classified into five major types, that is, (1) phenolic/lignin-derived compounds, (2) flavonoids, (3) nitroaromatics, (4) oxygenated aromatics, and (5) other chromophores. Identified chromophores account for ~23–64% of the total light absorption measured by the PDA detector in the wavelength range of 300–370 nm. In the representative samples from urban and remote areas, oxygenated aromatics and nitroaromatics dominate the absorption in the wavelengths below and above 320 nm, respectively. The highly polluted urban sample shows the most complex HPLC-PDA chromatogram, and more other chromophores contribute to the bulk absorption. Phenolic/ lignin-derived compounds are the most light-absorbing species in the soil-influenced sample. Chromophores in two remote samples exhibit ultraviolet–visible features distinct from other samples, which are attributed to flavonoids. Identification of individual chromophores and quantitative analysis of their optical properties are helpful for elucidating the roles of BrC in snow radiative balance and photochemistry.

54 ENVIRONMENTAL SCIENCES↗

3D Quantification of Pore Networks and Anthropogenic Carbon Mineralization in Stacked Basalt Reservoirs

Basalt formations are promising candidates for the geologic storage of anthropogenic CO 2 due to their storage capacity, porosity, permeability, and reactive geochemical trapping ability. The Wallula Basalt Carbon Storage Pilot Project demonstrated that supercritical CO 2 injected into >800 m deep Columbia River Basalt Group stacked reservoir flow tops mineralizes to ankerite-siderite-aragonite on month-year timescales, with 60% of the 977 metric tonnes of CO 2 converted within two years. The potential impacts of mineral precipitation and consequent changes on rock porosity, pore structure, pore size, and pore size distributions have likely been underestimated hitherto. Herein, we address these knowledge gaps using X-ray Micro Computed Tomography (XMT) to evaluate the pore network architecture of sidewall cores recovered two years after CO 2 injection. In the present study, we performed a detailed quantitative analysis of the CO 2 -reacted basalt cores by XMT imaging. Reconstructed 3D images were analyzed to study the distribution and volumetric details of porosity and carbonate nodules in the cores along with the various other phases, providing insight into paragenesis and carbonate growth mechanisms, including mineralogic/chemical zonation. Finally, these findings are being used to parametrize multiphase reactive transport models to predict the fate and transport of subsurface CO 2 , enabling scale-up to commercial-scale geologic carbon storage in basalts and other reactive mafic-ultramafic formations.

54 ENVIRONMENTAL SCIENCES↗

Rhenium-Sulfido and -Dithiolato Corroles: Reflections on Chalcophilicity

The high-temperature (~180 °C) reaction between free-base meso-triarylcorroles and Re 2 (CO) 10 , followed by exposure to PCl 3 and thiols (or elemental sulfur), affords rhenium-sulfido (ReS) corroles in 67-76% yields. The use of shorter reaction times, lower temperatures (~130 °C), and a dithiol (e.g., ethane-1,2-dithiol) also allows the isolation of rhenium-dithiolato corroles, presumptive intermediates on the path to ReS corroles. The ReS corroles exhibit high thermal stability and two reversible oxidations and reductions in their cyclic voltammograms, with redox potentials nearly identical to those observed for analogous ReO corroles. The electrochemical HOMO-LUMO gaps of the complexes, at 2.2 eV, are consistent with ligand-centered oxidation and reduction. The UV-vis spectra of ReS corroles, on the other hand, differ significantly from those of their ReO counterparts. Scalar-relativistic DFT calculations suggest that this difference reflects low-energy LUMO+2 and LUMO+3 levels, consisting of Re-S π-antibonding interactions; the ReO corroles, in contrast, exhibit a larger LUMO+1/LUMO+2 gap, as expected for a relatively classical Gouterman-type metalloporphyrin analogue. The high stability of ReS corroles is consistent with geochemists' view of rhenium as a moderately chalcophilic element (i.e., one that partitions into sulfide melts) as well as with a recent quantitative analysis of thiophilicity, which indicates that rhenium's oxophilicity and thiophilicity are essentially evenly balanced.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗