bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction
Authors: Franklinos T E 
Published: November 2024

AbstractThe Introduction begins from 2.1 and provides an account of Cynthia as Propertius’ scripta puella. It goes on to demonstrate that she is his amatory poetry enfleshed and that the account of his relationship with her—his lover’s discourse—can be closely mapped onto his articulation of his poetic stance as an elegist. In the course of his poetry, Propertius intratextually revisits and recasts his earlier elegies in later ones encoding a poetics of repetition; this is apparent throughout his corpus. The elegiac repetitiousness of language and theme is mirrored in the repetitive nature of the fragmented episodes of the amorous discourse that he construes with Cynthia and with which his reader is presented. It is also argued that, in turning back to revisit earlier books, Propertius integrates later books into his pre-existing corpus, while also reframing that corpus by the addition of new material.
Genomic architecture in social insects is more strongly associated with phylogeny than social behavior
Authors: Behrends Garrett , Hagan Thomas , Kuinkel Samir , Miller Sara E 
Published: November 2024

Abstract
The evolution of sociality in insects has been predicted to reduce effective population sizes, in turn leading to changes in genome architecture, including higher recombination rates, larger genomes, increased GC-biased gene conversion (gBGC), and greater intragenomic variation in GC content to maintain castes through differential methylation. As the number of sequenced insect genomes continues to grow, it remains an open question which, if any, of these genomic features are consistent across social insect genomes. A major challenge to determining such commonalities has been the lack of phylogenetically controlled analyses across independent origins of sociality. Of the 15 Hymenoptera species for which recombination rate was available, social species had higher rates of recombination. Next, we conducted a broader analysis of genome architecture by analyzing genome assemblies for 435 species of Hymenoptera and 8 species of Blattodea to test if GC content, genome size, distribution of CpG sites or codon bias repeatedly differed between social and nonsocial species. Overall, there was little support for predictable changes in genome architecture associated with sociality across Hymenoptera, after accounting for phylogenetic relationships. However, we found a significant negative relationship between sociality and GC content within the family Apidae and a significant negative relationship between sociality and genome size within the family Halictidae. In all, these results suggest that unique origins of social behavior may produce unique trends in genomic architecture. Our study highlights the need to examine genome architecture across independent origins of social behavior.
Functional analysis of a S-adenosylmethionine-insensitive methylenetetrahydrofolate reductase identified in methionine-accumulating yeast mutants
Authors: Isogai Shota , Nishimura Akira , Inoue Akiko , Sonohara Shino , Tsugukuni Takashi , Takagi Hiroshi 
Published: November 2024

Abstract
Essential amino acids (EAAs) are important for the maintenance of brain functions. Therefore, the yeast Saccharomyces cerevisiae that accumulates EAAs would help elderly people ingest appropriate levels of EAAs, which in turn could slow neurodegeneration, extend the healthy lifespan, and improve quality of life. Here, we isolated 2 mutant strains, ETH-80 and ETH-129, that accumulate the EAA methionine. Both strains were derived from a diploid laboratory yeast by conventional mutagenesis and carry a novel mutation in the MET13 gene, which encodes the Ser443Phe variant of methylenetetrahydrofolate reductase. Enzymatic analysis revealed that the Ser443Phe substitution abolished the sensitivity to S-adenosyl methionine (SAM)-mediated inhibition even in the presence of 2 m m SAM, while increasing the activity for NADPH-dependent reduction. Furthermore, yeast cells expressing the Ser443Phe variant showed a 4-fold increase in intracellular methionine content compared to the wild-type Met13. These findings will be useful for the future development of methionine-accumulating yeast strains.
PINK1-mediated mitophagy attenuates pathological cardiac hypertrophy by suppressing the mtDNA release-activated cGAS-STING pathway
Authors: Zhou Haobin , Wang Xiao , Xu Tianyu , Gan Daojing , Ma Zhuang , Zhang Hao , Zhang Jian , Zeng Qingchun , Xu Dingli 
Published: November 2024

Abstract

Aims
Sterile inflammation is implicated in the development of heart failure (HF). Mitochondria play important roles in triggering and maintaining inflammation. Mitophagy is important for regulation of mitochondrial quality and maintenance of cardiac function under pressure overload. The association of mitophagy with inflammation in HF is largely unclear. As PINK1 is a central mediator of mitophagy, our objective was to investigate its involvement in cardiac hypertrophy, and the effect of PINK1-mediated mitophagy on cGAS-STING activation during cardiac hypertrophy.

Methods and results
PINK1 knockout and cardiac-specific PINK1-overexpressing transgenic mice were created and subsequently subjected to transverse aortic constriction (TAC) surgery. In order to explore whether PINK1 regulates STING-mediated inflammation during HF, PINK1/STING (stimulator of interferon genes) double-knockout (DKO) mice were created. Pressure overload was induced by TAC. Our findings indicate a significantly decline in PINK1 expression in TAC-induced hypertrophy. Cardiac hypertrophic stimuli caused the release of mitochondrial DNA (mtDNA) into the cytosol, activating the cGAS-STING signalling, which in turn initiated cardiac inflammation and promoted the progression of cardiac hypertrophy. PINK1 deficiency inhibited mitophagy activity, promoted mtDNA release, and then drove the overactivation of cGAS-STING signalling, exacerbating cardiac hypertrophy. Conversely, cardiac-specific PINK1 overexpression protected against hypertrophy thorough inhibition of the cGAS-STING signalling. DKO mice revealed that the effects of PINK1 on hypertrophy were dependent on STING.

Conclusion
Our findings suggest that PINK1-mediated mitophagy plays a protective role in pressure overload-induced cardiac hypertrophy via inhibiting the mtDNA-cGAS-STING pathway.
Epitranscriptomic regulation of cardiac fibrosis via YTHDF1-dependent PIEZO2 mRNA m6A modification
Authors: Ding Ji-Fei , Tu Bin , Song Kai , Liu Zhen-Yu , Lin Li-Chan , Liu Zhi-Yan , Shi Yan , Yang Jing-Jing , Zhao Jian-Yuan , Tao Hui 
Published: November 2024

Abstract

Aims
Mechanosensitive (MS) ion channels play a key role in heart development, physiology, and disease. However, little is known about the molecular mechanisms of the MS non-selective cationic channel Piezo family in cardiac fibrosis.

Methods and results
Mice were treated with ISO/Ang-II/TAC to induce cardiac fibrosis. AAV9 carrying POSTN promoter-driven small hairpin RNA targeting YTHDF1, and Piezo2 were administered to ISO mice to investigate their roles in cardiac fibrosis. RNA-seq, single-cell sequencing, and histological and biochemical analyses were performed to determine the mechanism by which YTHDF1 regulates Piezo2 expression in cardiac fibrosis. Piezo2 was reconstituted in YTHDF1-deficient cardiac fibroblasts (CFs) and mouse hearts to study its effects on CF autophagy and fibrosis. Piezo2 but not Piezo1 expression increased in experimental cardiac fibrosis and TGF-β1-induced CFs. Fibroblast-specific Piezo2 deficiency ameliorated fibroblast activation and autophagy and inhibited cardiac fibrosis. Mechanistically, Piezo2 up-regulation was associated with elevated m6A mRNA levels. Site-specific m6A modifications at peak_26355 were crucial for regulating the binding of YTHDF1 to Piezo2 mRNA and inducing Piezo2 translation. Notably, Piezo2 epitranscriptomic repression ameliorated experimental cardiac fibrosis.

Conclusions
We demonstrated a novel epitranscriptomic mechanism through which YTHDF1 recognizes Piezo2 and controls cardiac fibroblast autophagy and fibrosis through m6A-dependent modulation. Our findings provide new insights for the development of preventive measures for cardiac fibrosis.
Was There a Crisis? Living Standards in Lower Canada, 1760 to 1848
Authors: Curtis Matthew , Geloso Vincent 
Published: November 2024

Abstract
Lower Canada, now the Canadian province of Quebec, is believed to have faced an agricultural crisis in the early 1800s, leading to declining living standards, a debated topic due to lack of data. This paper uses new data on real wages, literacy, and infant mortality to quantitatively assess living standards from 1760 to 1850. The findings show no evidence of a crisis; instead, there are only indications of improvements during the period.
Magnetic resonance imaging in patients with cardiac implantable electronic devices: the RESONANCE Spanish registry
Authors: Ruiz Mateas Francisco , Pérez Marcos Antonio , García López Fernando , González Susana , Anguera Camós Ignasi , Gusi Tragant Gabriel , Robledo Irrañitu María , Fernández Lozano Ignacio , Martínez Juan Gabriel , Alzueta Rodríguez Francisco Javier 
Published: November 2024

Abstract

Aims
Despite increasing evidence demonstrating the safety of magnetic resonance imaging (MRI) in patients with cardiac implantable electronic devices (CIEDs), this procedure is often neglected in this population. This Spanish registry aimed to determine the proportion of MRI referrals and performance among patients with pacemakers (PMs) or implantable cardioverter defibrillators (ICDs).

Methods and results
This prospective, multicentre, open-label registry involved 21 Spanish centres. Data were collected upon implant of PMs or ICDs from BIOTRONIK and one year after, and included the number of MRIs and computed tomography scans prescribed, performed and denied, and reasons for denial. Data from 1105 patients (mean age: 74.2 years) were analysed and 982 completed the follow-up. Of them, 82.2% had a PM and 17.8% an ICD. A total of 351 imaging tests were prescribed in 220 patients (19.9%), including 52 MRIs in 39 patients (3.5%) and 299 computed tomography scans in 196 patients (17.8%). Among the MRIs, 44 (84.6%) were performed, five (9.6%) were not performed, and three (5.8%) were replaced by an alternative test. Most of the indicated computed tomography scans were performed (97.7%). The proportion of patients with an MRI scan referral was 4.6% during the pre-COVID-19 period and 2.6% during the COVID-19 period. No MRI-related arrhythmic ventricular event was reported.

Conclusion
This registry revealed that only 3.5% of patients with CIEDs had an MRI referral over the study, with rates decreasing to 2.6% during the COVID-19 period. These rates contrast with the 85 MRIs conducted per 1000 inhabitants in Spain in 2020.
Shared environmental similarity between relatives influences heritability of reproductive timing in wild great tits
Authors: Jones Carys V , Regan Charlotte E , Cole Ella F , Firth Josh A , Sheldon Ben C 
Published: November 2024

Abstract
Intraspecific variation is necessary for evolutionary change and population resilience, but the extent to which it contributes to either depends on the causes of this variation. Understanding the causes of individual variation in traits involved with reproductive timing is important in the face of environmental change, especially in systems where reproduction must coincide with seasonal resource availability. However, separating the genetic and environmental causes of variation is not straightforward, and there has been limited consideration of how small-scale environmental effects might lead to similarity between individuals that occupy similar environments, potentially biasing estimates of genetic heritability. In ecological systems, environments are often complex in spatial structure, and it may therefore be important to account for similarities in the environments experienced by individuals within a population beyond considering spatial distances alone. Here, we construct multi-matrix quantitative genetic animal models using over 11,000 breeding records (spanning 35 generations) of individually-marked great tits (Parus major) and information about breeding proximity and habitat characteristics to quantify the drivers of variability in two key seasonal reproductive timing traits. We show that the environment experienced by related individuals explains around a fifth of the variation seen in reproductive timing, and accounting for this leads to decreased estimates of heritability. Our results thus demonstrate that environmental sharing between relatives can strongly affect estimates of heritability and therefore alter our expectations of the evolutionary response to selection.
Assembly of functional microbial ecosystems: from molecular circuits to communities
Authors: Wu Shengbo , Zhou Yongsheng , Dai Lei , Yang Aidong , Qiao Jianjun 
Published: November 2024

Abstract
Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate, or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, or promising applications. The strategies for coordinating microbial ecosystems based on different regulation circuits have not been systematically summarized, which calls for a more comprehensive framework for the assembly of microbial communities. In this review, we summarize diverse cross-talk and orthogonal regulation modules for de novo bottom-up assembling functional microbial ecosystems, thus promoting further consortia-based applications. First, we review the cross-talk communication-based regulations among various microbial communities from intra-species and inter-species aspects. Then, orthogonal regulations are summarized at metabolites, transcription, translation, and post-translation levels, respectively. Furthermore, to give more details for better design and optimize various microbial ecosystems, we propose a more comprehensive design-build-test-learn procedure including function specification, chassis selection, interaction design, system build, performance test, modeling analysis, and global optimization. Finally, current challenges and opportunities are discussed for the further development and application of microbial ecosystems.
On the reliability of constraining surface conductivity using induced polarization measurements in sedimentary rocks
Authors: Peshtani Klaudio , Slater Lee 
Published: November 2024

SUMMARY
Recent advances in understanding the induced polarization (IP) method have led to improvements in interpreting hydraulic properties from electrical measurements. Distinguishing the effect of surface conduction from conduction through the electrolyte filling the interconnected pore spaces has been an ongoing challenge in interpreting field-scale electrical resistivity data sets. Previously proposed mechanistic models have suggested that this limitation can be overcome by utilizing the coefficient that describes the ratio between IP measurements and surface conductivity. In this study, we examine this proportionality coefficient (ℓ) through the relationship between IP parameters (imaginary conductivity and normalized chargeability) and surface conductivity for a sample group of 98 sedimentary rocks, composed of sandstones, carbonates and mudstones. A strong linear relationship is observed between the IP parameters and surface conductivity. However, values of ℓ vary significantly across each sample group such that low-salinity estimates of formation factor (F) using the single universal estimate of ℓ are poor. Estimates of F for a single rock type (sandstone, carbonate or mudstone) are improved using ℓ values unique to that rock type, although F estimates for mudstones show high sensitivity to changes in ℓ. Using ℓ coefficients calibrated on a sample group with similar lithological properties to the investigated group moderately improves the estimation of F. Consistent with theory, no relationship is observed between the proportionality coefficient and the measured petrophysical parameters of the porous medium. Our results suggest that, although IP measurements provide a valuable field-scale proxy for surface conductivity, improving petrophysical predictions (i.e. in this case, estimating F) remains a challenge.
Reply: MIND the Gap: Psychiatric Conditions in Inflammatory Bowel Disease
Authors: Massironi Sara , Danese Silvio 
Published: November 2024

Lay Summary
This commentary clarifies the methodological approaches of a recently published systematic review and meta-analysis on psychiatric conditions in IBD, addressing limitations in data, subgroup analysis, and publication bias. It emphasizes the need for further primary research to better understand the psychiatric burden in IBD patients and improve study design.
Fecal and Sputum Microbiota and Treatment Response in Patients With Mycobacterium abscessus Pulmonary Disease
Authors: Kim Joong-Yub , An Sujin , Kim So Yeon , Bae Eunhye , Cho Yong-Joon , Kwak Nakwon , Kim Donghyun , Yim Jae-Joon 
Published: November 2024

Abstract

Background
The microbiota may provide biomarkers for clinical outcomes in chronic respiratory conditions, though its role in Mycobacterium abscessus pulmonary disease (PD) remains largely unknown. We aimed to identify microbial signatures in fecal and sputum microbiotas associated with treatment response in M abscessus PD.

Methods
We prospectively enrolled patients undergoing antibiotic therapy, collecting fecal and sputum samples at baseline, 2 weeks, and 6 months. Using 16S rRNA amplicon sequencing, we analyzed microbiota diversity and composition in early treatment responders and nonresponders, classified by sputum culture results at 2 weeks.

Results
Among 32 participants, 27 patients (median age, 66 years; 85.2% women; 48.1% with subspecies abscessus) were included for analysis. Fifteen patients (55.6%) achieved negative conversion at 2 weeks, sustained in 93.3% at 6 months. Responders showed signifcantly decreased fecal microbiota diversity at 2 weeks, unlike nonresponders (P = .029). Increased abundance of Eubacterium hallii in baseline fecal microbiota was indicative of unresponsiveness, whereas increased Enterococcus in feces at 2 weeks was linked with favorable response. In sputum, high baseline levels of Burkholderia-Caballeronia-Paraburkholderia and Porphyromonas, along with decreased Rothia at 2 weeks, were associated with good treatment response.

Conclusions
In M abscessus PD, changes in microbial diversity and compositional signatures reflect treatment response.
Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea
Authors: Takamiya Hinako , Kouduka Mariko , Kato Shingo , Suga Hiroki , Oura Masaki , Yokoyama Tadashi , Suzuki Michio , Mori Masaru , Kanai Akio , Suzuki Yohey 
Published: November 2024

Abstract
Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts and/or rock surfaces. To understand the ecology of rock-hosted DPANN archaea, rocks rather than fluids should be directly characterized. Here, we investigated a deep-sea hydrothermal vent chimney without fluid venting where our previous study revealed the high proportion of Pacearchaeota, one of the widespread and enigmatic lineages of DPANN archaea. Using spectroscopic methods with submicron soft X-ray and infrared beams, the microbial habitat was specified to be silica-filled pores in the inner chimney wall comprising chalcopyrite. Metagenomic analysis of the inner wall revealed the lack of biosynthetic genes for nucleotides, amino acids, cofactors, and lipids in the Pacearchaeota genomes. Genome-resolved metaproteomic analysis clarified the co-occurrence of a novel thermophilic lineage actively fixing carbon and nitrogen and thermophilic archaea in the inner chimney wall. We infer that the shift in metabolically active microbial populations from the thermophiles to the mesophilic DPANN archaea occurs after the termination of fluid venting. The infilling of mineral pores by hydrothermal silica deposition might be a preferred environmental factor for the colonization of free-living Pacearchaeota with ultrasmall cells depending on metabolites synthesized by the co-occurring thermophiles during fluid venting.
Impact of timing on the invasion of synthetic bacterial communities
Authors: Dooley Keven D , Henry Lucas P , Bergelson Joy 
Published: November 2024

Abstract
Microbial communities regularly experience ecological invasions that can lead to changes in composition and function. Factors thought to impact susceptibility to invasions, such as diversity and resource use, vary over the course of community assembly. We used synthetic bacterial communities to evaluate the success and impact of invasions occurring at different times during the community assembly process. Fifteen distinct communities were subjected to each of three bacterial invaders at the initial assembly of the community (“initial invasion”), 24 h into community assembly (“early invasion”), when the community was still undergoing transient dynamics, and 7 days into community assembly (“late invasion”), once the community had settled into its final composition. Communities were passaged daily and characterized through sequencing after reaching a stable composition. Invasions often failed to persist over time, particularly in higher richness communities. However, invasions had their largest effect on composition when they occurred before a community had settled into a stable composition. We found instances where an invader was ultimately excluded yet had profound and long-lasting effects on invaded communities. Invasion outcome was positively associated with lower community richness and resource use efficiency by the community, which varied throughout assembly. Our results demonstrate that microbial communities experiencing transient community dynamics are more affected by, and in some instances prone to, invasion, a finding relevant to efforts to modify the composition of microbial communities.
Diffusing Risk: Bureaucratic Agency, UN Security Council Horse-Trading, and the Role of Co-Financing
Authors: Jud Stefano 
Published: November 2024

Abstract
Political lending is problematic for the operations of multilateral development banks (MDBs) since politically motivated aid has a greater default risk than other aid projects. MDB bureaucrats, therefore, face a dilemma. On the one hand, they want to please major shareholders by engaging in political lending. On the other hand, they want to mitigate their MDB's exposure to excessive risk. One way to solve this dilemma is to share the risk of loans with other lenders through co-financing. I expect that as countries’ share of politically motivated aid increases, these countries’ portfolios will receive more co-financed loans. Using newly collected loan-level data from the European Bank for Reconstruction and Development, I find that UNSC membership increases the number of co-financed loans by 38.5 percent and increases the share of co-financed loans in a country's European Bank for Reconstruction and Development loan portfolio by 19.1 percentage points. I demonstrate that these results are consistent with the argument that MDB bureaucrats want to mitigate risk.