bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic analysis of pristine oil sheds new light on the global distribution of microbial genetic repertoire in hydrocarbon-associated ecosystems
Authors: Plewka Julia , Alibrandi Armando , Bornemann Till L V , Esser Sarah P , Stach Tom L , Sures Katharina , Becker Jannis , Moraru Cristina , Soares André , di Primio Rolando , Kallmeyer Jens , Probst Alexander J 
Published: January 2025

Abstract
Oil reservoirs are society’s primary source of hydrocarbons. While microbial communities in industrially exploited oil reservoirs have been investigated in the past, pristine microbial communities in untapped oil reservoirs are little explored, as are distribution patterns of respective genetic signatures. Here, we show that a pristine oil sample contains a complex community consisting of bacteria and fungi for the degradation of hydrocarbons. We identified microorganisms and their pathways for the degradation of methane, n-alkanes, mono-aromatic, and polycyclic aromatic compounds in a metagenome retrieved from biodegraded petroleum encountered in a subsurface reservoir in the Barents Sea. Capitalizing on marker genes from metagenomes and public data mining, we compared the prokaryotes, putative viruses, and putative plasmids of the sampled site to those from 10 other hydrocarbon-associated sites, revealing a shared network of species and genetic elements across the globe. To test for the potential dispersal of the microbes and predicted elements via seawater, we compared our findings to the Tara Ocean dataset, resulting in a broad distribution of prokaryotic and viral signatures. Although frequently shared between hydrocarbon-associated sites, putative plasmids, however, showed little coverage in the Tara Oceans dataset, suggesting an undiscovered mode of transfer between hydrocarbon-affected ecosystems. Based on our analyses, genetic information is globally shared between oil reservoirs and hydrocarbon-associated sites, and we propose that currents and other physical occurrences within the ocean along with deep aquifers are major distributors of prokaryotes and viruses into these subsurface ecosystems.
Draft genome sequence of the glasshouse-potato aphid Aulacorthum solani
Authors: Torres Joseph , Rozo-Lopez Paula , Brewer William , Saleh Ziabari Omid , Parker Benjamin J 
Published: January 2025

Abstract
Aulacorthum solani is a worldwide agricultural pest aphid capable of feeding on a wide range of host plants. This insect is a vector of plant viruses and causes injury to crops including stunted growth from the loss of phloem. We found that the publicly available genome for A. solani is contaminated with another aphid species, and we produced a new genome using a barcoded isogenic laboratory line. We generated Oxford Nanopore and Illumina reads to assemble a draft genome, and we sequenced RNA to aid in the annotation of our assembly. Our A. solani genome is 671 Mb containing 7,020 contigs with an N50 length of 196 kb with a BUSCO completeness of 98.6%. Out of the 24,981 genes predicted by EGAPx, 22,804 were annotated with putative functions based on homology to other aphid species. This genome will provide a useful resource for the community of researchers studying aphids from agricultural and genomic perspectives.
Functional Carbohydrate-Active Enzymes Acquired by Horizontal Gene Transfer from Plants in the Whitefly Bemisia tabaci
Authors: Colinet Dominique , Haon Mireille , Drula Elodie , Boyer Mathilde , Grisel Sacha , Belliardo Carole , Koutsovoulos Georgios D , Berrin Jean-Guy , Danchin Etienne G J 
Published: January 2025

Abstract
Carbohydrate-active enzymes involved in the degradation of plant cell walls and/or the assimilation of plant carbohydrates for energy uptake are widely distributed in microorganisms. In contrast, they are less frequent in animals, although there are exceptions, including examples of carbohydrate-active enzymes acquired by horizontal gene transfer from bacteria or fungi in several of phytophagous arthropods and plant-parasitic nematodes. Although the whitefly Bemisia tabaci is a major agricultural pest, knowledge of horizontal gene transfer–acquired carbohydrate-active enzymes in this phloem-feeding insect of the Hemiptera order (subfamily Aleyrodinae) is still lacking. We performed a comprehensive and accurate detection of horizontal gene transfer candidates in B. tabaci and identified 136 horizontal gene transfer events, 14 of which corresponding to carbohydrate-active enzymes. The B. tabaci horizontal gene transfer–acquired carbohydrate-active enzymes were not only of bacterial or fungal origin, but some were also acquired from plants. Biochemical analysis revealed that members of the glycoside hydrolase families 17 and 152 acquired from plants are functional beta-glucanases with different substrate specificities, suggesting distinct roles. These two carbohydrate-active enzymes are the first characterized glycoside hydrolase families 17 and 152 glucanases in an animal. We identified a lower number of horizontal gene transfer events in the related Aleyrodinae Trialeurodes vaporariorum, with only three horizontal gene transfer–acquired carbohydrate-active enzymes, including a glycoside hydrolase family 152 glucanase, with phylogenetic analysis suggesting a unique horizontal gene transfer event in the ancestor of the Aleyrodinae. Another glycoside hydrolase family 152 carbohydrate-active enzyme, most likely independently acquired from plants, was also identified in two plant cell-feeding insects of the Thysanoptera order, highlighting the importance of plant-acquired carbohydrate-active enzymes in the biology of piercing-sucking insects.
SlH3 and SlH4 promote multicellular Trichome formation and elongation by upregulating woolly in tomato
Authors: Kim Seong-Min , Choi Da-Min , Chun Jae-In , Kim Seong-Yeop , Kim Seong-Hyeon , Kim Jeong-Il , Jang Ji-in , Kim Keunhwa , Park Soon Ju , Seo Jang-Kyun , Jung Choonkyun , Kang Jin-Ho 
Published: January 2025

Abstract
Trichomes are tiny outgrowths on the plant epidermis that serve defensive purposes against various stresses. While the regulatory mechanisms underlying unicellular trichome development are well understood, those governing multicellular trichome formation remain largely unexplored. In this study, we reveal a new regulatory pathway involving the Hair3 (H3) and H4 genes, which encode C2H2 zinc finger proteins that participate in multicellular trichome development in tomato (Solanum lycopersicum). Using CRISPR-Cas9 to generate single- and double-knockout lines, we found that h3 and h4 single-mutant plants did not show altered trichome characteristics compared to wild-type plants. However, h3/h4 double-knockout plants displayed decreased densities of types I, VI, and VII trichomes, increased densities of types III and V trichomes, and reduced leaf and stem lengths of type I trichomes, revealing that H3 and H4 redundantly regulate trichome development. Notably, protein interaction assays demonstrated that H3 and H4 formed both homo- and hetero-dimers, supporting their cooperative role. Transcriptome and gene expression analyses identified H3 and H4 as key regulators of several genes involved in trichome development, including Woolly (Wo) and its downstream targets, such as Wox3b, MX1, H, and HD8. Protein-promoter assays showed that H3 and H4 did not directly bind to the Wo promoter but rather interacted with Wo, thereby enhancing the expression of Wo and Wox3b. These findings establish H3 and H4 as key regulators of trichome development and provide novel insights into the mechanisms controlling multicellular trichome development in tomato plants.
Cómo capturar el proceso de polarización judicial en contextos de declive democrático: la doctrina de la Suprema Corte mexicana sobre violaciones al procedimiento legislativo
Authors: Martín-Reyes Javier , Pozas-Loyo Andrea 
Published: January 2025

Abstract
This article contributes to the systematic study of judicial polarization in contexts of democratic decline. We argue that the two main empirical approaches to the study of polarization —the ideological and the affective— are limited in fully capturing the nature of judicial polarization in such processes because: (a) they fail to capture the nature of the dissent that defines this type of polarization, (b) they do not grasp the central role of high courts and (c) they fail to account for the incremental nature of these processes. To address these limitations, we propose an alternative methodology that allows us to measure and visually represent the polarization process in its different stages and to map the positions of judges in relation to different normative parameters. Finally, we apply this methodology to analyze the recent polarization of the Mexican Supreme Court by examining its doctrine on procedural violations in the legislative process.
Impact of Attaining an Aggressive Pharmacokinetic-Pharmacodynamic Target on the Clinical Efficacy of Continuous Infusion β-Lactam Therapy for Early Posttransplant Gram-Negative Infections in Critically Ill Orthotopic Liver Transplant Recipients: An Interim Analysis of a 3-Year Prospective, Observational Study
Authors: Gatti Milo , Rinaldi Matteo , Laici Cristiana , Bonazzetti Cecilia , Vizioli Luca , Ambretti Simone , Morelli Maria Cristina , Siniscalchi Antonio , Giannella Maddalena , Viale Pierluigi , Pea Federico 
Published: January 2025

Abstract

Background
To assess the impact of attaining aggressive β-lactam (BL) pharmacokinetic-pharmacodynamic (PK/PD) targets on clinical efficacy in critically ill orthotopic liver transplant (OLT) recipients with documented early gram-negative infections.

Methods
The study prospectively enrolled OLT recipients admitted to the posttransplant intensive care unit between June 2021 and May 2024; they had documented gram-negative infections treated with targeted therapy continuous infusion (CI) BLs and underwent therapeutic drug monitoring (TDM)-guided BL dosing adjustment within the first 72 hours. Aggressive PK/PD target attainment was measured. Multivariate logistic regression analyses were performed to test independent variables associated with 30-day resistance occurrence.

Results
Fifty critically ill OLT recipients were treated with CI BL in monotherapy (n = 34) or combination (n = 16) therapy for documented gram-negative infections No significant difference in clinical/microbiological outcome emerged between monotherapy and combination therapy. In 4 patients (8.0%), resistance developed within 30 days. At multivariate analysis, failure in attaining an aggressive BL PK/PD target emerged as the only independent predictor of 30-day resistance development (odds ratio, 14.33 [95% confidence interval, 1.46–140.53]; P = .02).

Conclusions
Attaining an aggressive PK/PD target with CI BLs in critically ill OLT recipients with documented gram-negative infections could represent an effective strategy for minimizing resistance occurrence to the selected BL.
Prevalence and concentration of aflatoxin M1 in milk and dairy products: an umbrella review of meta-analyses
Authors: Jahromi Abdolreza Sotoodeh , Jokar Mohammad , Abdous Arman , Rabiee Mohammad Hasan , Biglo Farzad Heydari Bahman , Rahmanian Vahid 
Published: January 2025

Abstract

Background
Aflatoxin M1 (AFM1) is a derivative of aflatoxin B1 and a significant contaminant of milk and dairy products. In this study, we implemented an umbrella review of all existing systematic reviews and meta-analyzing studies to apprise and summarize the worldwide prevalence and level of AFM1 in milk and dairy products.

Methods
We conducted a systematic review of structured review and meta-analysis articles published in English until January 2024, with no time limit. Articles were sourced from reputable databases, including PubMed/MEDLINE, EMBASE, Scopus, Web of Science, CINAHL and the Cochrane Database of Systematic Reviews. Relevant studies from Google Scholar were also included.

Results
The overall prevalence of AFM1 in all dairy products was 66.2% (95% CI 60.6 to 71.9%), with high heterogeneity (I²=99.7%, Q statistic=2221.03, p&lt;0.0001). The prevalence for specific dairy products was as follows: raw milk, 64.8% (95% CI 60.9 to 68.7%); pasteurized milk, 88.7% (95% CI 81.6 to 95.7%); sterilized milk, 71.0% (95% CI 67.2 to 74.8%); ultra-high temperature processing (UHT) milk, 67.9% (95% CI 64.9 to 70.9%); yogurt, 58.8% (95% CI 42.5 to 75.1%); doogh, 17.2% (95% CI 13.9 to 20.5%); and cheese 49.8% (95% CI 47.8 to 51.9%). The overall mean concentration of AFM1 across all dairy products was 57.22 ng/kg (95% CI 46.95 to 67.49), with significant heterogeneity (I²=99.7%, Q statistic=2221.03, p&lt;0.0001). Mean AFM1 levels (ng/kg) for each dairy product were as follows: raw milk, 52.51 (95% CI 40.96 to 64.05); pasteurized milk, 71.14 (95% CI 48.81 to 93.47); sterilized milk, 60.10 (95% CI 30.90 to 89.30); UHT milk, 82.57 (95% CI 35.30 to 129.85); yogurt, 46.74 (95% CI 24.27 to 69.21); and doogh, 41.60 (95% CI 32.60 to 50.60).

Conclusions
In total, these results highlight the importance of increasing the regulation of animal feed, reducing aflatoxin B1 (AFB1) in animal feed, and monitoring AFM1 in dairy products, particularly raw and heated milk.
Meta-omics reveals role of photosynthesis in microbially induced carbonate precipitation at a CO2-rich geyser
Authors: Violette Marlene J , Hyland Ethan , Burgener Landon , Ghosh Adit , Montoya Brina M , Kleiner Manuel 
Published: January 2025

Abstract
Microbially induced carbonate precipitation (MICP) is a natural process with potential biotechnological applications to address both carbon sequestration and sustainable construction needs. However, our understanding of the microbial processes involved in MICP is limited to a few well-researched pathways such as ureolytic hydrolysis. To expand our knowledge of MICP, we conducted an omics-based study on sedimentary communities from travertine around the CO2-driven Crystal Geyser near Green River, Utah. Using metagenomics and metaproteomics, we identified the community members and potential metabolic pathways involved in MICP. We found variations in microbial community composition between the two sites we sampled, but Rhodobacterales were consistently the most abundant order, including both chemoheterotrophs and anoxygenic phototrophs. We also identified several highly abundant genera of Cyanobacteriales. The dominance of these community members across both sites and the abundant presence of photosynthesis-related proteins suggest that photosynthesis could play a role in MICP at Crystal Geyser. We also found abundant bacterial proteins involved in phosphorous starvation response at both sites suggesting that P-limitation shapes both composition and function of the microbial community driving MICP.
Conspicuous Consumption in the Prairie House: A Veblenian Reading of Frank Lloyd Wright’s Highbacked Dining Chair
Authors: Merwood-Salisbury Joanna 
Published: January 2025

Abstract
Recent scholarship in the history of modern interior design has moved beyond the rhetoric of the avant-garde to recognize the enduring importance of style as an expression of social identity and taste as a mediator between design and broader cultural trends. This shift highlights the complex interplay between aesthetic choices and socio-cultural dynamics. As a case study of this interplay, this paper employs a Veblenian perspective—based on the work of economist Thorstein Veblen, notably his 1899 book The Theory of the Leisure Class—to reexamine one of the most iconic examples of modern furniture: Frank Lloyd Wright’s highbacked dining chair. Specifically, the paper explores the role of Wright’s chair in the context of the formal dining room of one of Wright’s largest Prairie-style houses, the Susan Lawrence Dana House in Springfield, Illinois, completed in 1903. Shifting focus from the production to the consumption of furniture, the paper investigates how Wright’s dining chairs defined the relationship between what Veblen called the “leisure” and “laboring” classes within this domestic realm. Viewed in situ, Wright’s iconic chair reveals a dichotomy deeply embedded within its design. While it was an advertisement for advanced industrial production, it also served as a luxury item created to fulfill the imperative of conspicuous consumption.
Evaluation of the biocontrol potential of Episyrphus balteatus (Diptera: Syrphidae) on wheat aphids in northern China
Authors: Jiang Shanshan , Liu Xiaoxia , Wu Kongming 
Published: January 2025

Abstract
Marmalada hoverfly, Episyrphus balteatus De Geer (Diptera: Syrphidae), is a cosmopolitan fly species providing pest control and pollination services. As wheat aphids cause significant losses to global wheat production, a systematic evaluation of the predatory potential and biocontrol service functions of E. balteatus in wheat ecosystems was undertaken. The daily maximum prey consumption of third instar E. balteatus on the adult of Rhopalosiphum padi Linnaeus, Schizaphis graminum Rondani, and Sitobion miscanthi Takahashi (Hemiptera: Aphididae) were 250, 500, and 100 individuals/third instar larvae, respectively. The S. graminum population decline rates in cages after release of the third instars at ratios of 1:100 and 1:200 were 100% and 94.17%, respectively, 72-h after exposure. Feeding assays involving R. padi, S. graminum, and S. miscanthi showed a DNA detectability half-life of 4.17, 6.44, and 4.83 h, respectively, in third instar larvae of E. balteatus. Using multiplex polymerase chain reaction-based gut content analysis to detect prey DNA remains, we confirmed that E. balteatus larvae preyed upon R. padi, S. graminum, S. miscanthi, and Metopolophium dirhodum Walker (Hemiptera: Aphididae) in the field experiments during 2022 to 2024. A significant positive correlation was also found between corrected prey detection rate and aphid population dynamics. These results provide an entry point for understanding the ecological service function of E. balteatus and developing the biological control strategy of the wheat aphid management.
Secrets of the Goo: The genome assembly of the Pacific banana slug, Ariolimax columbianus
Authors: Genetti Maximilian , Escalona Merly , Mirchandani Cade , Oppenheimer Jonas , Beraut Eric , Sacco Samuel , Seligmann William , Fairbairn Colin W , Sahasrabudhe Ruta , Marimuthu Mohan P A , Nguyen Oanh , Chumchim Noravit , Corbett-Detig Russell 
Published: January 2025

Abstract
The Pacific banana slug, Ariolimax columbianus, is endemic to the forests of the Pacific Northern West. Found throughout the coastal foothills and mountains of California, the hermaphroditic molluscs Ariolimax spp. are niche-constrained, hyper-localized, and phenotypically diverse. The evolutionary history, recent population history and environmental conditions leading to their phenotypic and genetic variation are not understood. To facilitate such research, we present the first high-quality de novo genome assembly of A. columbianus as part of the California Conservation Genomics Project. Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard California Conservation Genomics Project genome assembly protocol. This assembly comprises 401 scaffolds spanning 2.29 Gb, represented by a scaffold N50 of 94.9 Mb, a contig N50 of 3.7 Mb, and a benchmarking universal single-copy ortholog completeness score of 93.9%. Future work will use the A. columbianus genome to study the population structure of Ariolimax spp. across California to understand patterns of population structure, genetic diversity, and the broader ecological connections with their habitat. This data will contribute to the California Conservation Genomics Project, expanding the knowledge about the partitioning of genomic variation across the different ecoregions of California.
Low-dose quinine targets KCNH6 to potentiate glucose-induced insulin secretion
Authors: Xiong Feng-Ran , Zhu Juan-Juan , Zhu Xiao-Rong , Lu Jing , Yang Jin-Kui 
Published: January 2025

Abstract
Insulin secretion is mainly regulated by two electrophysiological events, depolarization initiated by the closure of ATP-sensitive K+ (KATP) channels and repolarization mediated by K+ efflux. Quinine, a natural component commonly used for the treatment of malaria, has been reported to directly stimulate insulin release and lead to hypoglycemia in patients during treatment through inhibiting KATP channels. In this study, we verified the insulinotropic effect of quinine on the isolated mouse pancreatic islets. We also revealed that low-dose quinine (&lt;20 µM) did not directly provoke Ca2+ spikes or insulin secretion under low-glucose conditions but potentiated Ca2+ influx and insulin secretion induced by high glucose, which cannot be explained by KATP inhibition. KCNH6 (hERG2) is a voltage-dependent K+ (Kv) channel that plays a critical role in the repolarization of pancreatic β cells. Patch clamp experiments showed that quinine inhibited hERG channels at low micromolar concentrations. However, whether quinine can target KCNH6 to potentiate glucose-induced insulin secretion remains unclear. Here, we showed that in vivo administration of low-dose quinine (25 mg/kg) improved glucose tolerance and increased glucose-induced insulin release in wild-type control mice but not in Kcnh6-β-cell-specific knockout (βKO) mice. Consistently, in vitro treatment of primary islet β cells with low-dose quinine (10 µM) prolonged action potential duration and augmented glucose-induced Ca2+ influx in the wild-type control group but not in the Kcnh6-βKO group. Our results demonstrate that KCNH6 plays an important role in low-dose quinine-potentiated insulin secretion and provide new insights into KCNH6-targeted drug development.
Beyond human flourishing: an argument for ecological education
Authors: Schinkel Anders 
Published: January 2025

Abstract
In this article I engage with the literature on human flourishing as an aim of education to argue that we need to look beyond human flourishing and embrace ecological education—an education that acknowledges and reflects the networks of interdependence of all that lives, including ourselves—inspired by an ecological ethic. The article is structured as follows. I begin by briefly introducing the problem and raising the question: is human flourishing too narrow an aim of education, from an ecological perspective? The next section discusses the value of human flourishing as an aim of education, recent objections, and rebuttals to those objections. I then turn to an ecological critique, arguing that the focus on human flourishing is ultimately (unjustifiably) anthropocentric. Even if human flourishing would require the flourishing of ecosystems, other species, biodiversity, and so on—which on standard conceptions of human flourishing is only partly true—ecological concerns cannot all be assumed to be implicit in human flourishing; and more importantly they should not be approached through human flourishing alone. I end by considering a pragmatic question: is ‘ecological flourishing’ still a plausible overarching aim (or justification) of education, or is it too far removed from the everyday reality of education and its individual and societal functions? I argue that it is fairly easy to make sense of in practical terms, and more easily embodied in concrete educational content and activities than ‘human flourishing’.