The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

Galaxies Going Bananas: Inferring the 3D Geometry of High-Redshift Galaxies with JWST-CEERS

The 3D geometry of high-redshift galaxies remains poorly understood. We build a differentiable Bayesian model and use Hamiltonian Monte Carlo to efficiently and robustly infer the 3D shapes of star-forming galaxies in JWST-CEERS observations with $\log M_*/M_{\odot}=9.0-10.5$ at $z=0.5-8.0$. We reproduce previous results from HST-CANDELS in a fraction of the computing time and constrain the mean ellipticity, triaxiality, size and covariances with samples as small as $\sim50$ galaxies. We find high 3D ellipticities for all mass-redshift bins suggesting oblate (disky) or prolate (elongated) geometries. We break that degeneracy by constraining the mean triaxiality to be $\sim1$ for $\log M_*/M_{\odot}=9.0-9.5$ dwarfs at $z>1$ (favoring the prolate scenario), with significantly lower triaxialities for higher masses and lower redshifts indicating the emergence of disks. The prolate population traces out a ``banana'' in the projected $b/a-\log a$ diagram with an excess of low $b/a$, large $\log a$ galaxies. The dwarf prolate fraction rises from $\sim25\%$ at $z=0.5-1.0$ to $\sim50-80\%$ at $z=3-8$. If these are disks, they cannot be axisymmetric but instead must be unusually oval (triaxial) unlike local circular disks. We simultaneously constrain the 3D size-mass relation and its dependence on 3D geometry. High-probability prolate and oblate candidates show remarkably similar S\'ersic indices ($n\sim1$), non-parametric morphological properties and specific star formation rates. Both tend to be visually classified as disks or irregular but edge-on oblate candidates show more dust attenuation. We discuss selection effects, follow-up prospects and theoretical implications.Comment: Submitted to ApJ, main body is 35 pages of which ~half are full-page figures, comments welcom

Global transpiration data from sap flow measurements : the SAPFLUXNET database

Plant transpiration links physiological responses of vegetation to water supply and demand with hydrological, energy, and carbon budgets at the land-atmosphere interface. However, despite being the main land evaporative flux at the global scale, transpiration and its response to environmental drivers are currently not well constrained by observations. Here we introduce the first global compilation of whole-plant transpiration data from sap flow measurements (SAPFLUXNET, https://sapfluxnet.creaf.cat/, last access: 8 June 2021). We harmonized and quality-controlled individual datasets supplied by contributors worldwide in a semi-automatic data workflow implemented in the R programming language. Datasets include sub-daily time series of sap flow and hydrometeorological drivers for one or more growing seasons, as well as metadata on the stand characteristics, plant attributes, and technical details of the measurements. SAPFLUXNET contains 202 globally distributed datasets with sap flow time series for 2714 plants, mostly trees, of 174 species. SAPFLUXNET has a broad bioclimatic coverage, with woodland/shrubland and temperate forest biomes especially well represented (80 % of the datasets). The measurements cover a wide variety of stand structural characteristics and plant sizes. The datasets encompass the period between 1995 and 2018, with 50 % of the datasets being at least 3 years long. Accompanying radiation and vapour pressure deficit data are available for most of the datasets, while on-site soil water content is available for 56 % of the datasets. Many datasets contain data for species that make up 90 % or more of the total stand basal area, allowing the estimation of stand transpiration in diverse ecological settings. SAPFLUXNET adds to existing plant trait datasets, ecosystem flux networks, and remote sensing products to help increase our understanding of plant water use, plant responses to drought, and ecohydrological processes. SAPFLUXNET version 0.1.5 is freely available from the Zenodo repository (https://doi.org/10.5281/zenodo.3971689; Poyatos et al., 2020a). The "sapfluxnetr" R package - designed to access, visualize, and process SAPFLUXNET data - is available from CRAN.Peer reviewe

Block-based syntax from context-free grammars

Block-based programming systems employ a jigsaw metaphor to write programs. They are popular in the domain of programming education (e.g., Scratch), but also used as a programming interface for end-users in other disciplines, such as arts, robotics, and configuration management. In particular, block-based environments promise a convenient interface for Domain-Specific Languages (DSLs) for domain experts who might lack a traditional programming education. However, building a block-based environment for a DSL from scratch requires significant effort. This paper presents an approach to engineer block-based language interfaces by reusing existing language artifacts. We present Kogi, a tool for deriving block-based environments from context-free grammars. We identify and define the abstract structure for describing block-based environments. Kogi transforms a context-free grammar into this structure, which then generates a block-based environment based on Google Blockly. The approach is illustrated with four case studies, a DSL for state machines, Sonification Blocks (a DSL for sound synthesis), Pico (a simple programming language), and QL (a DSL for questionnaires). The results show that usable block-based environments can be derived from context-free grammars, and with an order of magnitude reduction in effort

Electron Transfer Reactions of Copper Proteins

Copper proteins are a widespread and diverse class, isolated from plant, animal, bacterial, and fungal sources (1, 1a). The proteins considered here are involved in oxidation-reduction reactions, either as oxidoreductases or as electron carriers; other functions of copper proteins include metal ion storage and oxygen transport

Preparation and Spectroscopic Studies of Cobalt(II)-Stellacyanin

The cobalt(II) derivative of the “blue” copper protein stellacyanin has been prepared, and its visible-ultraviolet spectrum is reported. Tryptophan fluorescence quenching and p-mercuribenzoate titration results strongly suggest that Co(II) and Cu(II) compete for the same stellacyanin binding site and that a cysteine sulfur atom is coordinated in both cases. This interpretation is supported by the finding of an intense band at 355 nm in Co(II)-stellacyanin attributable to a charge transfer transition of the RS(-) → Co(II) type. The visible absorption spectrum of Co(II)-stellacyanin exhibits band maxima at 540, 625, and 655 nm. These bands are attributable to d-d transitions originating in a high-spin Co(II) center. It is suggested that a correspondence exists between charge transfer bands observed at 355 and 300 nm in the Co(II) derivative to those found at 604 and 450 nm in the native protein. It is concluded that the intense 604-nm peak in Cu(II)-stellacyanin is attributable to a cys-S → Cu(II) charge transfer transition