The general public and scientific community alike are abuzz over the release of ChatGPT and GPT-4. Among many concerns being raised about the emergence and widespread use of tools based on large language models (LLMs) is the potential for them to propagate biases and inequities. We hope to open a conversation within the environmental data science community to encourage the circumspect and responsible use of LLMs. Here, we pose a series of questions aimed at fostering discussion and initiating a larger dialogue. To improve literacy on these tools, we provide background information on the LLMs that underpin tools like ChatGPT. We identify key areas in research and teaching in environmental data science where these tools may be applied, and discuss limitations to their use and points of concern. We also discuss ethical considerations surrounding the use of LLMs to ensure that as environmental data scientists, researchers, and instructors, we can make well-considered and informed choices about engagement with these tools. Our goal is to spark forward-looking discussion and research on how as a community we can responsibly integrate generative AI technologies into our work.

“All or none” approaches to the use of contact precautions for methicillin-resistant Staphylococcus aureus (MRSA) both fail to recognize that transmission risk varies. This qualitative study assessed healthcare personnel perspectives regarding the feasibility of a risk-tailored approach to use contact precautions for MRSA more strategically in the acute care setting.

The most common equine tapeworm, Anoplocephala perfoliata, has often been neglected amongst molecular investigations and has been faced with limited treatment options. However, the recent release of a transcriptome dataset has now provided opportunities for in-depth analysis of A. perfoliata protein expression. Here, global, and sub-proteomic approaches were utilized to provide a comprehensive characterization of the A. perfoliata soluble glutathione transferases (GST) (ApGST). Utilizing both bioinformatics and gel-based proteomics, GeLC and 2D-SDS PAGE, the A. perfoliata ‘GST-ome’ was observed to be dominated with Mu class GST representatives. In addition, both Sigma and Omega class GSTs were identified, albeit to a lesser extent and absent from affinity chromatography approaches. Moreover, 51 ApGSTs were localized across somatic (47 GSTs), extracellular vesicles (EVs) (Whole: 1 GST, Surface: 2 GSTs) and EV depleted excretory secretory product (ESP) (9 GSTs) proteomes. In related helminths, GSTs have shown promise as novel anthelmintic or vaccine targets for improved helminth control. Thus, provides potential targets for understanding A. perfoliata novel infection mechanisms, host–parasite relationships and anthelmintic treatments.

Background: Clostridioides difficile infection (CDI) often recurs in patients aged ≥65 years and those with comorbidities. Clinical trials often exclude patients with history of immunosuppression, malignancy, renal insufficiency, or other comorbidities. In a phase 3 trial (ECOSPOR III), SER-109 was superior to placebo in reducing recurrent CDI (rCDI) risk at week 8 and was well tolerated. We report integrated safety data for SER-109 in a broad patient population through week 24 from phase 3 studies: ECOSPOR III and ECOSPOR IV. Methods: ECOSPOR III was a double-blind, placebo-controlled trial conducted in participants with ≥2 CDI recurrences randomized 1:1 to placebo or SER-109. ECOSPOR IV was an open-label, single-arm study conducted in 263 patients with rCDI enrolled in 2 cohorts: (1) rollover participants from ECOSPOR III with on-study recurrence and (2) participants with ≥1 CDI recurrence, inclusive of the current episode. In both studies, the investigational product was administered as 4 oral capsules over 3 days. Treatment-emergent adverse events (TEAEs) were collected through week 8; serious TEAEs and TEAEs of special interest (ie, bacteremia, abscess, meningitis) were collected through week 24. Results: In total, 349 participants received SER-109 in ECOSPOR III and/or ECOSPOR IV (mean age 64.2; 68.8% female). Chronic diseases included cardiac disease (31.2%), immunocompromised or immunosuppressed (21.2%), diabetes (18.9% ), and renal impairment or failure (13.2%). Overall, 221 (63.3%) of 349 participants who received SER-109 experienced TEAEs through week 24. Most were mild to moderate and gastrointestinal. The most common (>5% of participants) treatment related TEAEs were flatulence, abdominal pain and distension, decreased appetite, constipation, nausea, fatigue, and diarrhea. No participants experienced a treatment-related TEAE leading to study withdrawal. Invasive infections were observed in 28 participants (8%); those with identified pathogens were unrelated to SER-109 species, and all were deemed unrelated to treatment by the investigators. There were 11 deaths (3.2%) and 48 participants (13.8%) with serious TEAEs, none of which were deemed treatment related. There were no clinically important differences in the safety profile across subgroups of sex, race, prior antibiotic regimen, or number of CDI recurrences. No safety signals were observed in participants with renal impairment or failure, diabetes, cardiac disease, or immunocompromised or immunosuppressed individuals. Conclusions: In this integrated analysis of phase 3 trials, SER-109, an investigational microbiome therapeutic, was well tolerated in this vulnerable patient population with prevalent comorbidities. No infections, nor those with identified pathogens, were attributed to SER-109 or product species. This safety profile might be expected because this purified product is composed of spore-forming Firmicutes normally abundant in the healthy microbiome.

Financial support: This study was funded by Seres Therapeutics.

Disclosures: None

The term “blue justice” was coined in 2018 during the 3rd World Small-Scale Fisheries Congress. Since then, academic engagement with the concept has grown rapidly. This article reviews 5 years of blue justice scholarship and synthesizes some of the key perspectives, developments, and gaps. We then connect this literature to wider relevant debates by reviewing two key areas of research – first on blue injustices and second on grassroots resistance to these injustices. Much of the early scholarship on blue justice focused on injustices experienced by small-scale fishers in the context of the blue economy. In contrast, more recent writing and the empirical cases reviewed here suggest that intersecting forms of oppression render certain coastal individuals and groups vulnerable to blue injustices. These developments signal an expansion of the blue justice literature to a broader set of affected groups and underlying causes of injustice. Our review also suggests that while grassroots resistance efforts led by coastal communities have successfully stopped unfair exposure to environmental harms, preserved their livelihoods and ways of life, defended their culture and customary rights, renegotiated power distributions, and proposed alternative futures, these efforts have been underemphasized in the blue justice scholarship, and from marine and coastal literature more broadly. We conclude with some suggestions for understanding and supporting blue justice now and into the future.

A famous problem in birational geometry is to determine when the birational automorphism group of a Fano variety is finite. The Noether–Fano method has been the main approach to this problem. The purpose of this paper is to give a new approach to the problem by showing that in every positive characteristic, there are Fano varieties of arbitrarily large index with finite (or even trivial) birational automorphism group. To do this, we prove that these varieties admit ample and birationally equivariant line bundles. Our result applies the differential forms that Kollár produces on $p$-cyclic covers in characteristic $p > 0$.

Campeche, one of the Spanish Empire's main Mexican ports, was a place where previously distinct cultures and populations intermingled during the colonial era (AD 1540–1680). Investigation of the town's central plaza revealed a Hispanic cemetery of multi-ethnic burials. The authors combine previous analyses with newly generated genome-wide data from 10 individuals to trace detailed life histories of the mostly young, local Indigenous Americans and first-generation European and African immigrants, none of whom show evidence of genetic admixture. These results provide insights into the individual lives and social divides of the town's founder communities and demonstrate how ancient DNA analyses can contribute to understanding early colonial encounters.

The fossil record is notoriously imperfect and biased in representation, hindering our ability to place fossil specimens into an evolutionary context. For groups with fossil records mostly consisting of disarticulated parts (e.g., vertebrates, echinoderms, plants), the limited morphological information preserved sparks concerns about whether fossils retain reliable evidence of phylogenetic relationships and lends uncertainty to analyses of diversification, paleobiogeography, and biostratigraphy in Earth's history. To address whether a fragmentary past can be trusted, we need to assess whether incompleteness affects the quality of phylogenetic information contained in fossil data. Herein, we characterize skeletal incompleteness bias in a large dataset (6585 specimens; 14,417 skeletal elements) of fossil squamates (lizards, snakes, amphisbaenians, and mosasaurs). We show that jaws + palatal bones, vertebrae, and ribs appear more frequently in the fossil record than other parts of the skeleton. This incomplete anatomical representation in the fossil record is biased against regions of the skeleton that contain the majority of morphological phylogenetic characters used to assess squamate evolutionary relationships. Despite this bias, parsimony- and model-based comparative analyses indicate that the most frequently occurring parts of the skeleton in the fossil record retain similar levels of phylogenetic signal as parts of the skeleton that are rarer. These results demonstrate that the biased squamate fossil record contains reliable phylogenetic information and support our ability to place incomplete fossils in the tree of life.

To assess the burden of respiratory virus coinfections with severe acute respiratory coronavirus virus 2 (SARS-CoV-2), this study reviewed 4,818 specimens positive for SARS-CoV-2 and tested using respiratory virus multiplex testing. Coinfections with SARS-CoV-2 were uncommon (2.8%), with enterovirus or rhinovirus as the most prevalent target (88.1%). Respiratory virus coinfection with SARS-CoV-2 remains low 1 year into the coronavirus disease 2019 (COVID-19) pandemic.

The earliest stage in the innovation lifecycle, problem formulation, is crucial for setting direction in an innovation effort. When faced with an interesting problem, engineers commonly assume the approximate solution area and focus on ideating innovative solutions. However, in this project, NASA and their contracted partner, Accenture, collaboratively conducted problem discovery to ensure that solutioning efforts were focused on the right problems, for the right users, and addressing the most critical needs—in this case, exploring weather tolerant operations (WTO) to further urban air mobility (UAM) – known as UAM WTO. The project team leveraged generative, qualitative methods to understand the ecosystem, players, and where challenges in the industry are inhibiting development. The complexity of the problem area required that the team constantly observe and iterate on problem discovery, effectively “designing the design process.” This paper discusses the approach, methodologies, and selected results, including significant insights on the application of early-stage design methodologies to a complex, system-level problem.