bluuebunny/crossref_metadata_2025_split huggingface dataset:
Purple is the new green: biopigments and spectra of Earth-like purple worlds
Authors: Coelho Lígia Fonseca , Kaltenegger Lisa , Zinder Stephen , Philpot William , Price Taylor L , Hamilton Trinity L 
Published: April 2024

ABSTRACT
With more than 5500 detected exoplanets, the search for life is entering a new era. Using life on Earth as our guide, we look beyond green landscapes to expand our ability to detect signs of surface life on other worlds. While oxygenic photosynthesis gives rise to modern green landscapes, bacteriochlorophyll-based anoxygenic phototrophs can also colour their habitats and could dominate a much wider range of environments on Earth-like exoplanets. Here, we characterize the reflectance spectra of a collection of purple sulfur and purple non-sulfur bacteria from a variety of anoxic and oxic environments. We present models for Earth-like planets where purple bacteria dominate the surface and show the impact of their signatures on the reflectance spectra of terrestrial exoplanets. Our research provides a new resource to guide the detection of purple bacteria and improves our chances of detecting life on exoplanets with upcoming telescopes. Our biological pigment data base for purple bacteria and the high-resolution spectra of Earth-like planets, including ocean worlds, snowball planets, frozen worlds, and Earth analogues, are available online, providing a tool for modellers and observers to train retrieval algorithms, optimize search strategies, and inform models of Earth-like planets, where purple is the new green.
Observation uncertainty effects on the precision of interior planetary parameters
Authors: Plotnykov Mykhaylo , Valencia Diana 
Published: April 2024

ABSTRACT
Determining compositions of low-mass exoplanets is essential in understanding their origins. The certainty by which masses and radius are measured affects our ability to discern planets that are rocky or volatile rich. In this study, we aim to determine sound observational strategies to avoid diminishing returns. We quantify how uncertainties in mass, radius, and model assumptions propagate into errors in inferred compositions of rocky and water planets. For a target error in a planet’s iron-mass fraction or water content, we calculate the corresponding required accuracies in radius and mass. For instance, a rocky planet with a known radius error of 2 per cent (corresponding to TESS detection best errors) demands mass precision to be at 5–11 per cent to attain an 8 wt% precision in iron-mass fraction, regardless of mass. Similarly, a water world of equal radius precision requires 9–20 per cent mass precision to confine the water content within a 10 wt% margin. Lighter planets are more difficult to constrain, especially water-rich versus water-poor worlds. Studying Earth as an exoplanet, we find an ∼±5 point ’error floor’ in iron-mass fraction and ∼±7 in core-mass fraction from our lack of knowledge on mineralogy. The results presented here can quickly guide observing strategies to maximize insights into small exoplanet compositions while avoiding overobserving.
On data set tensions and signatures of new cosmological physics
Authors: Cortês Marina , Liddle Andrew R 
Published: April 2024

ABSTRACT
Can new cosmic physics be uncovered through tensions amongst data sets? Tensions in parameter determinations amongst different types of cosmological observation, especially the ‘Hubble tension’ between probes of the expansion rate, have been invoked as possible indicators of new physics, requiring extension of the ΛCDM paradigm to resolve. Within a fully Bayesian framework, we show that the standard tension metric gives only part of the updating of model probabilities, supplying a data co-dependence term that must be combined with the Bayes factors of individual data sets. This shows that, on its own, a reduction of data set tension under an extension to ΛCDM is insufficient to demonstrate that the extended model is favoured. Any analysis that claims evidence for new physics solely on the basis of alleviating data set tensions should be considered incomplete and suspect. We describe the implications of our results for the interpretation of the Hubble tension.
DNA sequence data, multispecies coalescent and morphometrics shed new light on the systematics of Iberian islamiinae springsnails (Caenogastropoda: Hydrobiidae)
Authors: Delicado Diana , Miller Jonathan P , García-Guerrero Fernando , Arconada Beatriz , Ramos Marian A 
Published: April 2024

ABSTRACT
Multilocus phylogenies have shown that soft-part anatomy alone is insufficient for the systematics of valvatiform- and trochiform-shelled springsnails of the subfamily Islamiinae (family Hydrobiidae) due to morphological similarities between taxa that are not closely related. However, a solid knowledge of their systematics and species boundaries is crucial to conserve this highly imperilled group. Here, we inferred molecular phylogenies based on two mitochondrial and two nuclear gene fragments from representatives of three morphological species of the Iberian genus Iberhoratia and performed multispecies coalescent and shell variation analyses (geometric morphometrics) to reevaluate their taxonomic status. The resulting phylogenetic analyses, which included homologous sequences of 15 other valvatiform-shelled hydrobiid species endemic to the Iberian Peninsula, depicted the topotypical specimens of I. aurorae and I. gatoa elisai distantly related to one another and the type species I. morenoi. Considering their high genetic divergence and morphological differences from other hydrobiid taxa, we have placed the former two species in the new genera Beatrix n. gen. and Actenidia n. gen. The multispecies coalescent delimitation method DELINEATE, a novel approach to the taxonomy of the Hydrobiidae, and shell morphometric data suggested two species within the ‘I. gatoa elisai’ clade. Based on morphological and molecular evidence, we recognized this clade as Actenidia, a new genus comprising the species A. elisai n. gen., n. comb. and A. baetica n. gen., n. sp. Our results underscore the importance of using multiple lines of evidence to delimitate species of Islamiinae and interpret their systematics. We also discuss the implications of our findings for conserving I. gatoa.
Activity reconstitution of Kre33 and Tan1 reveals a molecular ruler mechanism in eukaryotic tRNA acetylation
Authors: Ma Chun-Rui , Liu Na , Li Hong , Xu Hong , Zhou Xiao-Long 
Published: April 2024

Abstract
RNA acetylation is a universal post-transcriptional modification that occurs in various RNAs. Transfer RNA (tRNA) acetylation is found at position 34 (ac4C34) in bacterial tRNAMet and position 12 (ac4C12) in eukaryotic tRNASer and tRNALeu. The biochemical mechanism, structural basis and functional significance of ac4C34 are well understood; however, despite being discovered in the 1960s and identification of Kre33/NAT10 and Tan1/THUMPD1 as modifying apparatuses, ac4C12 modification activity has never been reconstituted for nearly six decades. Here, we successfully reconstituted the ac4C12 modification activity of yeast Kre33 and Tan1. Biogenesis of ac4C12 is primarily dependent on a minimal set of elements, including a canonical acceptor stem, the presence of the 11CCG13 motif and correct D-arm orientation, indicating a molecular ruler mechanism. A single A13G mutation conferred ac4C12 modification to multiple non-substrate tRNAs. Moreover, we were able to introduce ac4C modifications into small RNAs. ac4C12 modification contributed little to tRNA melting temperature and aminoacylation in vitro and in vivo. Collectively, our results realize in vitro activity reconstitution, delineate tRNA substrate selection mechanism for ac4C12 biogenesis and develop a valuable system for preparing acetylated tRNAs as well as non-tRNA RNA species, which will advance the functional interpretation of the acetylation in RNA structures and functions.
Cdc13 exhibits dynamic DNA strand exchange in the presence of telomeric DNA
Authors: Nickens David G , Feng Zhitong , Shen Jiangchuan , Gray Spencer J , Simmons Robert H , Niu Hengyao , Bochman Matthew L 
Published: April 2024

Abstract
Telomerase is the enzyme that lengthens telomeres and is tightly regulated by a variety of means to maintain genome integrity. Several DNA helicases function at telomeres, and we previously found that the Saccharomyces cerevisiae helicases Hrq1 and Pif1 directly regulate telomerase. To extend these findings, we are investigating the interplay between helicases, single-stranded DNA (ssDNA) binding proteins (ssBPs), and telomerase. The yeast ssBPs Cdc13 and RPA differentially affect Hrq1 and Pif1 helicase activity, and experiments to measure helicase disruption of Cdc13/ssDNA complexes instead revealed that Cdc13 can exchange between substrates. Although other ssBPs display dynamic binding, this was unexpected with Cdc13 due to the reported in vitro stability of the Cdc13/telomeric ssDNA complex. We found that the DNA exchange by Cdc13 occurs rapidly at physiological temperatures, requires telomeric repeat sequence DNA, and is affected by ssDNA length. Cdc13 truncations revealed that the low-affinity binding site (OB1), which is distal from the high-affinity binding site (OB3), is required for this intermolecular dynamic DNA exchange (DDE). We hypothesize that DDE by Cdc13 is the basis for how Cdc13 ‘moves’ at telomeres to alternate between modes where it regulates telomerase activity and assists in telomere replication.
Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes
Authors: Abdel-Fattah Wael R , Carlsson Mattias , Hu Guo-Zhen , Singh Ajeet , Vergara Alexander , Aslam Rameen , Ronne Hans , Björklund Stefan 
Published: April 2024

Abstract
Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2–8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3′-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3′-ends, overlapping the Lsm3 binding sites ∼250 bp downstream of their last intron–exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.
Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool
Authors: Letunic Ivica , Bork Peer 
Published: April 2024

Abstract
The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the management, display, annotation and manipulation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 6 introduces a modernized and completely rewritten user interface, together with numerous new features. A new dataset type has been introduced (colored/labeled ranges), greatly upgrading the functionality of the previous simple colored range annotation function. Additional annotation options have been implemented for several existing dataset types. Dataset template files now support simple assignment of annotations to multiple tree nodes through substring matching, including full regular expression support. Node metadata handling has been greatly extended with novel display and exporting options, and it can now be edited interactively or bulk updated through annotation files. Tree labels can be displayed using multiple simultaneous font styles, with precise positioning, sizing and styling of each individual label part. Various bulk label editing functions have been implemented, simplifying large scale changes of all tree node labels. iTOL’s automatic taxonomy assignment functions now support trees based on the Genome Taxonomy Database (GTDB), in addition to the NCBI taxonomy. The functionality of the optional user account pages has been expanded, simplifying the management, navigation and sharing of projects and trees. iTOL currently handles more than one and a half million trees from &gt;130 000 individual user accounts.
Deep carbon recycling viewed from global plate tectonics
Authors: Zhang Maoliang , Xu Sheng , Sano Yuji 
Published: April 2024

ABSTRACT
Plate tectonics plays an essential role in the redistribution of life-essential volatile elements between Earth's interior and surface, whereby our planet has been well tuned to maintain enduring habitability over much of its history. Here we present an overview of deep carbon recycling in the regime of modern plate tectonics, with a special focus on convergent plate margins for assessing global carbon mass balance. The up-to-date flux compilation implies an approximate balance between deep carbon outflux and subduction carbon influx within uncertainty but remarkably limited return of carbon to convecting mantle. If correct, carbon would gradually accumulate in the lithosphere over time by (i) massive subsurface carbon storage occurring primarily in continental lithosphere from convergent margins to continental interior and (ii) persistent surface carbon sinks to seafloors sustained by high-flux deep CO2 emissions to the atmosphere. Further assessment of global carbon mass balance requires updates on fluxes of subduction-driven carbon recycling paths and reduction in uncertainty of deep carbon outflux. From a global plate tectonics point of view, we particularly emphasize that continental reworking is an important mechanism for remobilizing geologically sequestered carbon in continental crust and sub-continental lithospheric mantle. In light of recent advances, future research is suggested to focus on a better understanding of the reservoirs, fluxes, mechanisms, and climatic effects of deep carbon recycling following an integrated methodology of observation, experiment, and numerical modeling, with the aim of decoding the self-regulating Earth system and its habitability from the deep carbon recycling perspective.
Up with Categories, Down with Sets; Out with Categories, In with Sets!
Authors: Kirby Jonathan 
Published: April 2024

Abstract
Practical approaches to the notions of subsets and extension sets are compared, coming from broadly set-theoretic and category-theoretic traditions of mathematics. I argue that the set-theoretic approach is the most practical for ‘looking down’ or ‘in’ at subsets and the category-theoretic approach is the most practical for ‘looking up’ or ‘out’ at extensions, and suggest some guiding principles for using these approaches without recourse to either category theory or axiomatic set theory.
A 10-year analysis of application and match rates for pain medicine training in the United States
Authors: Silvestre Jason , Nagpal Ameet 
Published: April 2024

Abstract

Objective
We analyzed application and match rates for pain medicine training in the United States and hypothesized that there would be (1) greater growth in the number of training positions than applicants, (2) higher match rates among US allopathic graduates relative to non-US allopathic graduates, and (3) greater number of unfilled training positions over time.

Design
Retrospective, cross-sectional study of all applicants for pain medicine training in the United States.

Method
National Resident Matching Program data were obtained over a ten-year period (2014-2023). Match rates and applicant-to-position ratios were calculated and compared over time with linear regression. Comparisons were made with chi-square tests.

Results
Growth in the number of annual training positions (261-377, 44% increase) exceeded growth in the number of interested applicants (398-415, 4% increase) (P &lt; .001). Annual applicant-to-training position ratios decreased (1.5-1.1, P &lt; .001). The representation of US allopathic graduates among incoming pain medicine fellows decreased over the study period (73%-58%, P &lt; .001) while US osteopathic graduates increased (9%-28%, P &lt; .001).
Match rates increased for both US allopathic graduates (71%-91%, P &lt; .001) and non-US allopathic graduates (51%-81%, P &lt; .001). From 2018 to 2023, US allopathic graduates (79%) had higher match rates than US osteopathic graduates (60%, P &lt; .001) and international medical graduates (57%, P &lt; .001). More available annual training positions went unfilled over the study period (2%-5%, P = .006).

Conclusions
Stagnant annual applicant volume and increasing number of available training positions have led to increasing match rates for pain medicine fellowship training. Fewer US allopathic graduates are pursuing pain medicine training. The increasing percentage of unfilled training positions warrants ongoing surveillance.
Validation of three health literacy screening questions compared with S-TOFHLA in a low-income diverse English- and Spanish-Speaking population
Authors: Kincaid Hope , Coyne Cathy A , Hamadani Roya , Friel Timothy 
Published: April 2024

Abstract

Background
Clinicians need a tool to gauge patients’ ability to understand health conditions and treatment options. The Short-form Test of Functional Health Literacy in Adults (S-TOFHLA) is the gold standard for this, but its length is prohibitive for use in clinical settings. This study seeks to validate a novel three-item question set for predicting health literacy.

Methods
This cross-sectional study utilized an in-person questionnaire alongside the S-TOFHLA. The sample included 2027 English- and Spanish-speaking adults (≥18 years) recruited from primary care practices serving a low-income eastern Pennsylvania community. Most patients (57.7%) identified as Hispanic. Diagnostic accuracy of each question and aggregated scores were assessed against the validated survey by calculating the area under the receiver operating characteristic (AUROC) curve.

Results
Questions in the ‘Problems Learning’ and ‘Help Reading’ domains (AUROC 0.66 for each) performed better than the ‘Confident Forms’ question (AUROC 0.64). Summing all three scores resulted in an even higher AUROC curve (0.71). Cronbach’s alpha of the combined items was 0.696.

Conclusions
Study results suggest that any of the three questions are viable options for screening health literacy levels of diverse patients in primary care clinical settings. However, they perform better as a summed score than when used individually.
Do investors care about biodiversity?
Authors: Garel Alexandre , Romec Arthur , Sautner Zacharias , Wagner Alexander F 
Published: April 2024

Abstract
This article introduces a new measure of a firm’s negative impact on biodiversity, the corporate biodiversity footprint (CBF), and studies whether it is priced in an international sample of stocks. On average, the CBF does not explain the cross-section of returns between 2019 and 2022. However, a biodiversity footprint premium (higher returns for firms with larger footprints) began emerging in October 2021 after the Kunming Declaration, which capped the first part of the UN Biodiversity Conference (COP15). Consistent with this finding, stocks with large footprints lost value in the days after the Kunming Declaration. The launch of the Taskforce on Nature-related Financial Disclosures (TNFD) in June 2021 had a similar effect. These results indicate that investors have started to require a risk premium upon the prospect of, and uncertainty about, future regulation or litigation to preserve biodiversity.
Long-term Changes in Personal Recovery and Quality of Life Among Patients With Schizophrenia Spectrum Disorders and Different Durations of Illness: A Meta-analysis
Authors: de Winter Lars , Jelsma Auke , Vermeulen Jentien M , van Weeghel Jaap , Hasson-Ohayon Ilanit , Mulder Cornelis L , Boonstra Nynke , Veling Wim , de Haan Lieuwe 
Published: April 2024

Abstract

Background and Hypothesis
In schizophrenia spectrum disorders (SSD) personal recovery and subjective quality of life (S-QOL) are crucial and show conceptual overlap. There is limited knowledge about how these outcomes change over time. Therefore, we investigated changes in personal recovery or S-QOL for patients with SSD. We specifically focused on the influence of the patients’ durations of illness (DOI) on changes in personal recovery and S-QOL.

Study Design
We included 46 studies investigating longitudinal changes in quantitative assessments of personal recovery or S-QOL for patients with SSD. Outcomes were categorized in overall personal recovery, overall S-QOL connectedness, hope and optimism, identity, meaning in life, and empowerment. We evaluated effect sizes of change between baseline and follow-up assessments. We also evaluated potential moderating effects, including DOI on these changes in outcomes.

Study Results
We found small improvements of overall personal recovery and S-QOL, but marginal or no improvement over time in the other more specific outcome domains. Patients without a schizophrenia diagnosis, a younger age, and more recent publications positively influenced these changes. We found no significant influence of DOI on the changes in any outcome domain.

Conclusions
Improvement in personal recovery or S-QOL of people with SSD is modest at best. However, these studies did not fully capture the personal narratives or nonlinear process of recovery of an individual. Future research should focus on how to shift from a clinical to more person-oriented approach in clinical practice to support patients in improving their personal process of recovery.

Review protocol registration
CRD42022377100.
A review of soybean processing byproducts and their use in swine and poultry diets
Authors: Gaffield Katelyn N , Goodband Robert D , DeRouchey Joel M , Tokach Mike D , Woodworth Jason C , Denny Gordon , Gebhardt Jordan T 
Published: April 2024

Abstract
Due to its importance in animal feed, soybean meal has been extensively studied to optimize its use in livestock diets. Despite extensive research, the industry has not fully characterized specific areas of soybean processing such as the inclusion of soybean byproducts added back to soybean meal during processing. Soybean processing byproducts can encompass a large variety of materials including weeds and foreign material, soybean hulls, gums, soapstocks, lecithins, spent bleaching clays, and deodorizer distillates. Despite the potential for being added back to soybean meal when a crushing plant is integrated with an oil refinery, there is currently limited information on the composition of many of these soybean processing byproducts and their subsequent effects on soybean meal quality and animal performance. Therefore, there may be opportunities for a new area of research focused on soybean processing byproducts and their optimal use within the livestock feed industry. This review summarizes the current information on soybean byproducts with a focus on identifying the areas with the greatest potential for future research in swine and poultry nutrition.