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At least 163 records · Page 9

Accurate segmentation of localized corrosion in structural alloys via deep learning

This study presents a deep learning-based approach for the automated segmentation of corrosion damage in scanning electron microscopy (SEM) images. The proposed method enables rapid and accurate segmentation of corrosion features in these SEM images, making it highly suitable for real-time applications such as automated microscopy. Specifically, a dedicated corrosion segmentation database tailored for this task is constructed. The newly constructed dataset, alongside data from two public databases, are employed to jointly train a deep learning-based model modified with a texture refinement module. Compared to the same model without the texture refinement module, the refined model substantially enhances the efficacy and efficiency of corrosion segmentation. Furthermore, the methodology developed here is extendable to segmentation tasks for other materials with similar resolution, texture, and contrast characteristics, thereby paving the way for accelerated and automated analysis in corrosion science and beyond.

Artificial Intelligence↗

Joint Factorization of QCD and QED Radiation in Lepton-Hadron Scattering

The factorization theorem plays an important role in the analysis of high energy quantum chromodynamic (QCD) processes, separating the nonperturbative hadronic interaction into the universal parton distribution functions (PDFs) and fragmentation functions (FFs) and the process-dependent interactions into short distance perturbative calculations, with any interference power suppressed. With a virtual photon exchange, lepton-hadron deep inelastic scattering (DIS) provides an electromagnetic hard probe for the partonic structure of colliding hadrons and has played an important role in the development of QCD factorization. However, the collision induced QED radiation can change the momentum of the exchanged but unobserved virtual photon, making the photon-hadron frame, where the factorization formalism for DIS and semi-inclusive DIS (SIDIS) was derived, ill defined. A new analogous factorization approach has been introduced to separate the leading power process-independent QED radiative contributions to the single photon exchange by introducing lepton distribution functions (LDFs) and lepton fragmentation functions (LFFs), while process-dependent effects are perturbatively calculated with large logarithms removed [J. High Energ. Phys. 2021, 157 (2021)]. These LDFs and LFFs are considered global, as they appear in many different interactions, such as e+e-, DIS and SIDIS, so data from experiments can be used to fit and describe these functions across a wide range of lepton scattering. In this work, I will apply this new hybrid factorization approach to lepton-hadron DIS and SIDIS. For DIS, I derive the NLO short distance perturbative contribution to the cross section and demonstrate the effects the QED radiation has on the cross section using this approach using the CTEQ parameterization for the QCD functions. As part of the SIDIS analysis, I study the cross-section in two different kinematic regions: (1) the scattered lepton and observed hadron are not near back-to-back, and (2) they are close to back-to-back, where collinear QCD factorization works for (1) and TMD QCD factorization for (2) while collinear QED factorization works for both. As part of this work, I show the effects on the SIDIS cross section using fixed order calculations for the unpolarized structure function by first showing the effect of the radiative corrections on the main kinematic variables, especially how the internal transverse momentum is significantly correlated to the external angular dependence, and then the unpolarized structure function (or cross section) with matching between the descriptions for low and high transverse momentum. This work will impact the calculations for predictions for data from COMPASS and various Jefferson Lab experiments.

Cammarota, Justin [Univ. of Kentucky, Lexington, K↗

Dark Energy Survey Year 3 Results: Cosmological Constraints from Cluster Abundances, Weak Lensing, and Galaxy Clustering

Galaxy clusters provide a unique probe of the late-time cosmic structure and serve as a powerful independent test of the $\Lambda$CDM model. This work presents the first set of cosmological constraints derived with ~16,000 optically selected redMaPPer clusters across nearly 5,000 $\rm{deg}^2$ using DES Year 3 data sets. Our analysis leverages a consistent modeling framework for galaxy cluster cosmology and DES-Y3 joint analyses of galaxy clustering and weak lensing (3x2pt), ensuring direct comparability with the DES-Y3 3x2pt analysis. We obtain constraints of $S_8 = 0.864 \pm 0.035$ and $\Omega_{\rm{m}} = 0.265^{+0.019}_{-0.031}$ from the cluster-based data vector. We find that cluster constraints and 3x2pt constraints are consistent under the $\Lambda$CDM model with a Posterior Predictive Distribution (PPD) value of $0.53$. The consistency between clusters and 3x2pt provides a stringent test of $\Lambda$CDM across different mass and spatial scales. Jointly analyzing clusters with 3x2pt further improves cosmological constraints, yielding $S_8 = 0.811^{+0.022}_{-0.020}$ and $\Omega_{\rm{m}} = 0.294^{+0.022}_{-0.033}$, a $24\%$ improvement in the $\Omega_{\rm{m}}-S_8$ figure-of-merit over 3x2pt alone. Moreover, we find no significant deviation from the Planck CMB constraints with a probability to exceed (PTE) value of $0.6$, significantly reducing previous $S_8$ tension claims. Finally, combining DES 3x2pt, DES clusters, and Planck CMB places an upper limit on the sum of neutrino masses of $\sum m_\nu < 0.26$ eV at 95% confidence under the $\Lambda$CDM model. These results establish optically selected clusters as a key cosmological probe and pave the way for cluster-based analyses in upcoming Stage-IV surveys such as LSST, Euclid, and Roman.

79 ASTRONOMY AND ASTROPHYSICS↗

A genomic perspective on fungal diversity and evolution

Originating from aquatic unicellular ancestors, over the course of ~1 billion years, the fungi have evolved to occupy nearly all aerobic environments on the planet, diversified into millions of different ‘species’ and have developed complex multicellular structures. Their relatively small, simple genomes have facilitated massive-scale sequencing and allowed us to explore genome evolution across an ancient eukaryotic kingdom. With thousands of genomes from diverse lineages now available, this Review will discuss insights into fungal biology and evolution gleaned with genomics and other multi-omics approaches. Using published genomes available through GenBank and the Joint Genome Institute’s MycoCosm platform, we generated kingdom-wide phylogenies and used them to highlight how fungal genomes have changed over time. With this phylogeny as a guide, we also discuss major evolutionary transitions that occurred across the fungal kingdom. Although progress has been made, these efforts are hampered by biases in genome representation and limited characterization of gene functions. Here, in this study, we discuss these challenges and possible future directions to address them, including initiatives to characterize conserved genes of unknown function and scale up sequencing towards 10,000 annotated fungal genomes.

Mondo, Stephen J. [USDOE Joint Genome Institute (J↗

The Power of DESI for Photometric Redshift Calibration: A Case Study with KiDS-1000

Accurate redshift estimates are a critical requirement for weak lensing surveys and one of the main uncertainties in constraints on dark energy and large-scale cosmic structure. In this paper, we study the potential to calibrate photometric redshift (photo-z) distributions for gravitational lensing using the Dark Energy Spectroscopic Instrument (DESI). Since beginning its science operations in 2021, DESI has collected more than 50 million redshifts, adding about one million monthly. In addition to its large-scale structure samples, DESI has also acquired over 256k high-quality spectroscopic redshifts (spec-zs) in the COSMOS and XMM and VVDS fields. This is already a factor of 3 larger than previous spec-z calibration compilations in these two regions. Here, we explore calibrating photo-zs for the subset of KiDS-1000 galaxies that fall into joint self-organizing map (SOM) cells overlapping the DESI COSMOS footprint using the DESI COSMOS observations. Estimating the redshift distribution in KiDS-1000 with the new DESI data, we find broad consistency with previously published results while also detecting differences in the mean redshift in some tomographic bins with an average shifts of Delta Mean(z) = -0.028 in the mean and Delta Median(z) = +0.011 in the median across tomographic bins. However, we also find that incompleteness per SOM cell, i.e., groups of galaxies with similar colors and magnitudes, can modify n(z) distributions. Finally, we comment on the fact that larger photometric catalogs, aligned with the DESI COSMOS and DESI XMM and VVDS footprints, would be needed to fully exploit the DESI dataset and would extend the coverage to nearly eight times the area of existing 9-band photometry.

Blanco, Diana [UC, Santa Cruz; UC, Santa Cruz, Ins↗

Measuring local primordial non-Gaussianity from the clustering of DESI DR1 LRGs and QSOs

We report the first measurement of primordial non-Gaussianity (PNG), parameterized by $f_{\mathrm{NL}}$, in the configuration space two-point correlation function (2pcf). We employ simulation based modeling and a novel approach for the mitigation of imaging systematics. We apply this method to samples of luminous red galaxies (LRG) and quasars (QSO) observed by the Dark Energy Spectroscopic Instrument (DESI) during the first year of its observations (DR1). The observed 68% CL interval on $f_{\mathrm{NL}}$ is $-3^{+22}_{-21}$ using LRGs, and $ 0^{+17}_{-16}$ using QSOs. The joint measurement yields $f_{\mathrm{NL}} = -3^{+12}_{-12}$ at $\ [68\%]$ CL. Our pipeline imposes a Gaussian prior on the value of $p$ (which defines the PNG bias via the Universality relation), with $p_{\rm LRG} = 1.0 \pm 0.1$ and $p_{\rm QSO} = 1.6\pm 0.1$. The observed constraining power of DESI tracers significantly exceeds that of previous large-scale structure (LSS) surveys, and encouragingly, approaches the sensitivity of CMB probes of PNG.

Brown, Z. [Kansas State U.]↗

Interfacial Hydrogen-Bond Dynamics in Transition Metal Compounds

Understanding how water behaves when confined within atomic layers of active transition-metal carbides, nitrides, and carbonitrides is essential for uncovering the fundamental principles needed to engineer solid–liquid interfaces at the atomic scale. Yet, how lattice element chemistry and surface termination groups collectively regulate the structure and mobility of such interlayer water remains poorly understood. Here, we present a composition-controlled investigation of interlayer water dynamics in layered transition-metal nitride, carbide, and carbonitride systems using a systematic integration of quasi-elastic neutron scattering (QENS), ab initio molecular dynamics (AIMD) simulations, and density functional theory (DFT) calculations. QENS measurements show that nitride-rich systems host mobile, translationally diffusing water with thermally activated self-diffusion coefficients on the order of 10 –10 m 2 s –1 , whereas mixed C/N lattices confine water to localized, nontranslational motion that is insensitive to temperature. AIMD and DFT reveal that lattice C/N chemistry and surface functional group composition reshape the first hydration layer by modulating the surface electronic structure and termination-dependent hydrogen-bond networks, leading to pronounced differences in water ordering and thermal resilience. On the other hand, fully carbide systems exhibit intermediate behavior, highlighting that water mobility is not primarily controlled by the hydration level alone but by the coupling between lattice composition and surface chemistry. Overall, this study establishes how surface chemistry and lattice composition jointly control interfacial hydrogen bond dynamics, offering a mechanistic framework for designing transition-metal layered materials with tailored interfacial transport properties.

Hydration↗

A highly active Burkholderia polyketoacyl-CoA thiolase for production of triacetic acid lactone

Triacetic acid lactone (TAL) is a versatile platform chemical traditionally biosynthesized via decarboxylative Claisen condensation by 2-pyrone synthase. However, this route is limited by poor efficiency and dependence on malonyl-CoA. Here, we show that non-decarboxylative Claisen condensation by polyketoacyl-CoA thiolases offers a more efficient alternative. Through mining homologs of a previously reported enzyme from Cupriavidus necator, we identify five thiolases with TAL production activity. One candidate, BktBbr from Burkholderia sp. RF2-non_BP3, exhibits approximately 30-fold higher activity in vitro and supports 30-fold higher TAL titers in Escherichia coli compared to the original enzyme. Fed-batch fermentation achieves titers up to 2.8 g L⁻¹. Structural analysis of BktBbr co-crystallized with CoA esters guides rational engineering to further enhance performance. Our discovery of a highly active thiolase establishes an alternative enzymatic route to produce TAL efficiently, providing a scalable foundation for sustainable biomanufacturing.

Wang, Zilong [Joint BioEnergy Institute (JBEI), Em↗

Maximum a posteriori Ly α estimator (MAPLE): band power and covariance estimation of the 3D Ly α forest power spectrum

We present a novel maximum a posteriori estimator to jointly estimate band powers and the covariance of the three-dimensional power spectrum (P3D) of Ly $\alpha$ forest flux fluctuations, called MAPLE. Our Wiener-filter based algorithm reconstructs a window-deconvolved P3D in the presence of complex survey geometries typical for Ly $\alpha$ surveys that are sparsely sampled transverse to and densely sampled along the line of sight. We demonstrate our method on idealized Gaussian random fields with two selection functions: (i) a sparse sampling of 30 background sources per square degree designed to emulate the current Dark Energy Spectroscopic Instrument; (ii) a dense sampling of 900 background sources per square degree emulating the upcoming Prime Focus Spectrograph Galaxy Evolution Survey. Our proof-of-principle shows promise, especially since the algorithm can be extended to marginalize jointly over nuisance parameters and contaminants, i.e. offsets introduced by continuum fitting. Our code is implemented in JAX and is publicly available on GitHub.

79 ASTRONOMY AND ASTROPHYSICS↗

Identification and Classification of Fungal GPCR Gene Families

G protein-coupled receptors (GPCRs) are transmembrane proteins crucial for signal transduction in eukaryotes, responding to diverse extracellular signals. Researchers have found and systematically summarized 14 distinct types of GPCRs in fungi but their distribution among numerous fungal species remained largely unexamined. Additionally, three families of mammalian homologs (Rhodopsin, Glutamate, and Frizzled) have been found in previous studies, but they are not included in the systematic classification of fungal GPCRs. Our study establishes a unified classification of 17 GPCR classes in fungi, combining 14 fungal and 3 mammalian previously recognized groups, and classifies 28,294 GPCRs across 1357 fungal species, significantly expanding the scale of GPCRs in fungi and demonstrating their broader distribution. We found that mammalian homologs are notably more prevalent in Early Diverging Fungi (EDF), whereas the previous 14 classes are predominantly found in Ascomycota and Basidiomycota. The most abundant class detected in fungi was Pth11-like GPCRs, exclusively found in Pezizomycotina and involved in fungal pathogenicity. Our analysis suggested that Pezizomycotina ancestor possessed an extensive array of Pth11-like GPCRs, but over time, some species underwent considerable reductions in these GPCRs in conjunction with genome contractions. Utilizing a custom-built convolutional neural network (CNN) for the identification of fungal GPCRs, we identified several putative novel fungal GPCRs. Predicted interactions between these prospective new GPCRs and G-alpha proteins, as simulated by AlphaFold Multimer, provided additional support for their functional relevance. In conclusion, our work defines the first large-scale, unified classification of fungal GPCRs, reveals lineage-specific expansions and contractions, and uncovers previously unrecognized GPCR candidates with potential functional roles in fungal signaling.

G protein-coupled receptors↗

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗

Resist! : Sustaining forest carbon sequestration and wood production after insect disturbance

Disturbances from insect pests threaten ecologically and economically important goods and services supplied by forests, including wood production and carbon sequestration. We highlight the factors that influence these services’ resistance, a term quantifying the initial response to disturbance. Insects inflict damage through a range of mechanisms, prompting distinct plant physiological responses that scale to influence ecosystem processes and, with time, goods and services. The degree and timing of tree mortality and defoliation affect the amount of residual vegetation available to support compensatory wood production and influence carbon sequestration by changing rates of detritus-fueled decomposition. Compounding, or sequential, insect attacks may prime a forest for additional disturbance, further eroding wood production and carbon sequestration. Forest management practices that promote biological and structural diversity, and augment or retain limiting biological and nutrient resources, may buffer against the effects of insect pests on wood production and carbon sequestration.

Gough, Christopher M. [Virginia Commonwealth Univ.↗

Polyhalohydrins: Investigating Vicinal Functionalities by Ring-Opening of Epoxides on Polyolefins

Halohydrins are functional groups that are underexplored in polymer science. This study synthesized and examined structure–property relationships of halohydrin-functionalized polymers derived from polycyclooctene (PCOE), which was obtained via ring-opening metathesis polymerization (ROMP). The polyhalohydrins, including polychlorohydrin, polybromohydrin, and polyiodohydrin, were produced through a two-step process involving epoxidation of PCOE followed by epoxide ring-opening using hydrochloric, hydrobromic, or hydroiodic acid. These stereoirregular and regioirregular polymers are amorphous as measured by differential scanning calorimetry and X-ray scattering. Lap joint shear testing revealed an enhanced adhesive performance in polychlorohydrin and polybromohydrin, with the former demonstrating nearly three times the ultimate shear stress compared to a model polyethylene, hydrogenated PCOE. Additionally, contact angle measurements and surface free energy analysis showed an increase in hydrophilicity and polarity from iodine- to bromine- to chlorine-functionalized polyhalohydrins, aligning with trends in adhesion strength. Furthermore, these results underscore the potential of halohydrin functionalization as a versatile approach for tuning surface properties, offering new opportunities for polymer-to-polymer transformations.

Functional groups↗

Map-level baryonification: unified treatment of weak lensing two-point and higher-order statistics

Precision cosmology benefits from extracting maximal information from cosmic structures, motivating the use of higher-order statistics (HOS) at small spatial scales. However, predicting how baryonic processes modify matter statistics at these scales has been challenging. The baryonic correction model (BCM) addresses this by modifying dark-matter-only simulations to mimic baryonic effects, providing a flexible, simulation-based framework for predicting both two-point and HOS. We show that a 3-parameter version of the BCM can jointly fit weak lensing maps' two-point statistics, wavelet phase harmonics coefficients, scattering coefficients, and the third and fourth moments to within 2% accuracy across all scales ℓ < 2000 and tomographic bins for a DES-Y3-like redshift distribution ( z ≲ 2), using the FLAMINGO simulations. These results demonstrate the viability of BCM-assisted, simulation-based weak lensing inference of two-point and HOS, paving the way for robust cosmological constraints that fully exploit non-Gaussian information on small spatial scales.

79 ASTRONOMY AND ASTROPHYSICS↗

Seed coat transcriptomic profiling of 5-593, a genotype important for genetic studies of seed coat color and patterning in common bean ( Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.) market classes have distinct seed coat colors, which are directly related to the diverse flavonoids found in the mature seed coat. To understand and elucidate the molecular mechanisms underlying the regulation of seed coat color, RNA-Seq data was collected from the black bean 5-593 and used for a differential gene expression and enrichment analysis from four different seed coat color development stages. 5-593 carries dominant alleles for 10 of the 11 major genes that control seed coat color and expression and has historically been used to develop introgression lines used for seed coat genetic analysis. Pairwise comparison among the four stages identified 6,294 differentially expressed genes (DEGs) varying from 508 to 5,780 DEGs depending on the compared stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that phenylpropanoid biosynthesis, flavonoid biosynthesis, and plant hormone signal transduction comprised the principal pathways expressed during bean seed coat pigment development. Transcriptome analysis suggested that most structural genes for flavonoid biosynthesis and some potential regulatory genes were significantly differentially expressed. Further studies detected 29 DEGs as important candidate genes governing the key enzymatic flavonoid biosynthetic pathways for common bean seed coat color development. Additionally, four gene models, Pv5-593.02G016100, 593.02G078700, Pv5-593.02G090900, and Pv5-593.06G121300, encode MYB-like transcription factor family protein were identified as strong candidate regulatory genes in anthocyanin biosynthesis which could regulate the expression levels of some important structural genes in flavonoid biosynthesis pathway. These findings provide a framework to draw new insights into the molecular networks underlying common bean seed coat pigment development.

60 APPLIED LIFE SCIENCES↗

Joint cosmic density reconstruction from photometric and spectroscopic samples

ABSTRACT We reconstruct the dark matter density field from spatially overlapping spectroscopic and photometric redshift catalogues through a field-level forward modelling approach. Instead of directly inferring the underlying density field, we find the best-fitting initial Gaussian fluctuations that will evolve into the observed cosmic volume. To account for the substantial uncertainty of photometric redshifts we employ a differentiable continuous Poisson process. As an initial test, we construct a mock based on the upcoming Prime Focus Spectrograph combined with photometric sample modelled on the Subaru Hyper Suprime-Cam. Depending on the statistic of interest, we find improvements in cosmic structure classification equivalent to 50–100 per cent more spectroscopic targets by combining relatively sparse spectroscopic with dense photometric samples.

Horowitz, B.↗

Integrated modeling of alpha particle losses in JET DT plasmas

Alpha particle confinement is crucial for sustaining burning plasmas and designing future reactor concepts. Along with classical/prompt losses, various magnetohydrodynamic instabilities can lead to wave-particle interactions which can transport alpha particles outward from the plasma. This can result in a reduction in plasma heating/performance, and, at worst, damage in-vessel components. Joint European Torus’s recent deuterium–tritium campaigns in 2021–2023 have produced numerous alpha particle loss measurements with its scintillator probe and Faraday cup array fast ion loss detectors as discussed in Bonofiglo et al (2024 Nucl. Fusion 64 096038). This paper will report on integrated energetic particle transport modeling in support of those measurements. The modeling is accomplished with the TRANSP and ORBIT-kick codes with the use of recently developed reduced models which calculate mode structure, amplitude, and the evolving dynamics. When possible, constraints and comparisons to experiment are conducted. Case studies are performed on a variety of magnetohydrodynamic activity, including: fishbones, tearing modes (TMs), and sawtooth crashes. Additionally, a special case of an alpha-driven toroidal Alfvén eigenmode is briefly discussed, where modeling showed marginally weak alpha losses and was unable to support experimental observations. Coupled effects between a TM and toroidal field ripple are presented and were unable to replicate the observations in lost particle pitch but did duplicate the localized flattening of the measured neutron profile. Additional modeling results compare the magnitude of losses and energy/velocity-space sensitivities against experimental observations/measurements for each scenario. This work corroborates numeric alpha transport modeling while also identifying model deficiencies. While this report details alpha transport, it also presents open issues for discussion in assessing the validity of our numerical models towards burning plasmas.

Bonofiglo, Phillip J. [Princeton Plasma Physics La↗

p-Type BiVO 4 for Solar O 2 Reduction to H 2 O 2

Photoelectrochemical cells (PECs) can directly utilize solar energy to drive chemical reactions to produce fuels and chemicals. Oxide-based photoelectrodes in general exhibit enhanced stability against photocorrosion, which is a critical advantage for building a sustainable PEC. However, most oxide-based semiconductors are n-type, and p-type oxides that can be used as photocathodes are limited. In this study, we report the synthesis, characterization, and application of p-type BiVO 4 with a monoclinic scheelite (ms) structure. ms-BiVO 4 is inherently n-type, and it has been investigated only as a photoanode to date. In this study, we prepared p-type ms-BiVO 4 (bandgap of 2.4 eV) via atomic doping of Ca 2+ at the Bi 3+ site under an O 2 -rich environment and examined its performance as a photocathode. We then demonstrated that the Ca-doped ms-BiVO 4 photocathode can be used for solar O 2 reduction to H 2 O 2 when coupled with appropriate catalysts. Our computational investigation using hybrid density functional theory revealed that holes are stable as polarons in ms-BiVO 4 and have a low self-trapping energy, that may lead to free carriers in the valence band at finite temperature. Our calculations also show that Ca is an effective shallow acceptor dopant with low formation energy and thermal ionization energy leading to p-type conductivity. In conclusion, our joint experimental and computational results provide critical insights into the design of p-type ms-BiVO 4 , enabling its use as a polaronic oxide photocathode.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗