bluuebunny/crossref_metadata_2025_split huggingface dataset:
Where the microbes aren't
Authors: Cockell Charles S 
Published: December 2024

Abstract
Although a large fraction of Earth’s volume and most places beyond the planet lack life because physical and chemical conditions are too extreme, intriguing scientific questions are raised in many environments within or at the edges of life’s niche space in which active life is absent. This review explores the environments in which active microorganisms do not occur. Within the known niche space for life, uninhabited, but habitable physical spaces potentially offer opportunities for hypothesis testing, such as using them as negative control environments to investigate the influence of life on planetary processes. At the physico-chemical limits of life, questions such as whether spaces devoid of actively metabolizing or reproducing life constitute uninhabitable space or space containing vacant niches that could be occupied with appropriate adaptation are raised. We do not know the extent to which evolution has allowed life to occupy all niche space within its biochemical potential. The case of habitable extraterrestrial environments and the scientific and ethical questions that they raise is discussed.
The government of Agnès of France, daughter of Saint Louis and duchess of Burgundy (c. 1260–1325)
Authors: Bardey David 
Published: December 2024

Abstract
Agnès de France (1260–1325), who was the youngest daughter of Saint Louis and Marguerite de Provence, is a little-known princess. She was, however, a remarkable political figure, whose role in government in the late thirteenth and early fourteenth centuries demonstrates the vital influence of Capetian royal women. After marrying Robert II of Burgundy (duke from 1272–1306) in 1273, Agnès became duchess of Burgundy and was involved in the administration of this duchy for over half a century. Her influence was especially significant during the rule of her sons, the dukes Hugues V (1306–15) and Eudes IV (1315–49). In light of this, it is important to try to understand how she obtained power and to delineate the characteristics of female government in this period, above all during her widowhood. The aims of this article are thus to shed new light on Agnès’ career and to explore the foundations of her power, that were interlinked with her various positions as a woman: daughter of King Louis XI, wife of Duke Robert II and mother of the dukes Hugues V and Eudes IV.
Long-term Effects of Local Area New Deal Work Relief in Childhood on Late Life Depression
Authors: Modrek Sepideh , Rehkopf David H 
Published: December 2024

Abstract

Objective
To investigate whether childhood exposure to local area New Deal emergency employment work relief activity was associated with lower depressive symptoms in late life.

Methods
This study utilized individual-level data from the Wisconsin Longitudinal Study (WLS) linked to the full count 1940 census. New Deal emergency employment programs were the largest non-wartime expansion in government led infrastructure, services, and employment policy in U.S. history. We used within county variation in WLS participants' exposure to emergency employment work relief activity during childhood (ages 0-3) to examine its association with depressive symptoms in late life. We examined depressive symptoms at three ages, 53-55, 65-67, and 72-74 but with a focus on depressive symptoms at ages 72-74 as a marker for late-life depression.

Results
Children who lived in neighborhoods with moderate or high levels of emergency employment work relief activity exhibited 14-18% lower depressive symptom scores at ages 72-74 compared to those from neighborhoods with low activity. These findings were consistent across various measures of late-life depressive symptoms, different model specifications, and after accounting for prior depressive symptoms.

Discussion
The study highlights the long-term mental health benefits of economic policies aimed at mitigating concentrated economic downturns among the most impacted individuals. Childhood exposure to New Deal work relief reduced depressive symptoms in older age, particularly new onsets of depressive symptoms at ages 72-74. These results suggest social policies aimed at maintaining economic activity in downturns can have long-term positive impacts on population mental health.
A numerical study of electrokinetically generated pre-earthquake geoelectric fields in layered porous media
Authors: Zheng Xu-Zhen , Ren Hengxin , Ren Qinhan , Huang Qinghua , Chen Xiaofei 
Published: December 2024

SUMMARY
The investigation into the physical mechanisms and behaviour of geoelectric fields as potential precursors of earthquakes is a crucial yet challenging task in seismo-electromagnetics. Assuming the electrokinetic effect as a potential mechanism, we propose a novel numerical modelling algorithm based on the framework of the Luco-Apsel-Chen generalized reflection and transmission method to explore the behaviour of geoelectric fields in stratified porous media during earthquake preparation. This algorithm incorporates two innovative aspects: (1) employing the Jordan decomposition to address the degeneracy problem encountered in the quasi-static regime, and (2) utilizing digital linear filters for Hankel transforms to conduct the wavenumber integration. The accuracy of the algorithm in computing static displacements in an extremely low porosity half-space model is verified through comparison with analytical solutions. Numerical results from a half-space model demonstrate a strong consistency between the behaviour of the vertical electric field and filtration displacements. Notably, the maximum amplitude of the vertical electric field can reach approximately 3150.5 mV km−1, which is detectable by receivers located at considerable distances from the epicentre. In addition, three distinct types of pre-earthquake electric fields are identified: (1) the localized electric field induced by slow P waves, (2) the interface electric responses and (3) the direct converted electric field from the source. Results from a multilayer porous model show the significant influence of the water table on the amplitude of the vertical electric field. This can be attributed to the influence of water saturation and permeability on the coefficient that combines the vertical electric field and the vertical filtration displacement. We also analyse the temporal evolution of different fields during earthquake preparation, which demonstrates a robust correlation between the temporal characteristics of pore pressure and that of the vertical electric field. This indicates that the vertical electric field offers an effective means to detect pore pressure evolution. Furthermore, our analysis demonstrates that the broadening of electric anomalies can be used to roughly estimate the rate of stress accumulation. The sensitivity of the electric signal to the strike, rake and dip angles of potential faults indicates its ability to determine fault geometry related to an impending earthquake. These observations underscore the potential of using geoelectric precursors to study earthquake preparation mechanisms.
Transitional Justice and the Problem of Democratic Decline
Authors: Dancy Geoff , Thoms Oskar Timo 
Published: December 2024

ABSTRACT∞
When transitional justice emerged as a field of practice amid the third wave of democracy, many hoped it would reinforce the rules and norms that prevent democratic decline. However, over half of all the democracies that transitioned from autocracy or experienced civil war in the last half-century have since undergone backsliding or breakdown. Is transitional justice partly to blame? This article theorizes six ways that transitional justice might contribute to democratic decline, or alternatively, to democratic progress. It then analyzes data from 118 democratic spells in 89 countries spanning 1970 to 2023 to evaluate which hypotheses are plausible. In line with theories focused on endogenous change, the findings suggest that transitional justice is actually associated with stronger electoral and judicial institutions, which reinforces the guardrails of democracy against autocratic reversion. Yet, while transitional justice might help prevent full democratic breakdown, it does not hinder democratic backsliding, particularly that which is driven by government restrictions on civic association.
Efficient Iterative Solutions for the Anisotropic Eikonal Equation in Seismic Wave Propagation Analysis
Authors: Liu Jianfeng , Lu Yongming , Lei Tao , Zhang Jiangjie , Zang Nan 
Published: December 2024

Abstract
The computation of traveltimes for compressional (P) waves is significantly important for earthquake and seismic exploration applications. The eikonal equation, functioning as a fundamental tool in seismic wave propagation analysis, plays a crucial role in the computation of traveltimes and the construction of seismic images. However, the inherent nonlinearity of the eikonal equation introduces complexity, particularly when addressing anisotropic media. The eikonal equation derived directly from Christoffel equation is applicable for general anisotropic traveltime calculations. However, its equation is a complex quartic equation, presenting significant challenges in the solving process. The selection of a fast and efficient iterative method is important in addressing these challenges. Additionally, determining the initial point for iterative method is also crucial for their stability and effectiveness. Finally, three numerical examples are presented to test the bisection, Newton, and secant methods for solving anisotropic equations, based on the characteristics of locally constructed solutions.
High-resolution studies of the C-band and L-band radio continuum of the periodic methanol maser source G9.62+0.20E and surrounding sources
Authors: Woode B , Hoare M G , Kuditcher A , Goedhart S 
Published: December 2024

ABSTRACT
High-resolution observations of the C-band and L-band radio continuum of the hypercompact H ii region $\rm G 9.62$+$\rm 0.20 E$ conducted with the e-MERLIN interferometric array are presented. A flux density of $\rm 2.25 \pm 0.20$ $\rm mJy$ and an angular size of $\rm 127 \pm 22$ $\rm mas$ were measured for the C-band continuum. At L band, an upper limit of $\rm 162$ $\rm \mu Jy$ on the integrated flux density was calculated at the continuum’s position. The surrounding sources C and D were detected at levels consistent with previous detections. The results for source E requires a steeper spectrum at L band than previous observations extrapolated from higher frequencies. This can be explained with a truncated inverse square law density distribution model. We obtain a C-band peak brightness temperature of about $\rm {4000\, \rm {K}}$, which assuming an electron temperature of $\rm {10^{4}}$$\rm {K}$ translates to an optical depth of $\rm {0.5}$, indicating the continuum is optically thin at C band going thick at L band. These results therefore place firm constraints on H ii region models in source E. The periodic variability of methanol masers, as seen in $\rm G 9.62$+$\rm 0.20 E$, has been explained with the pulsating star, accretion disc, and colliding wind binary models. Some models predict a hypercompact H ii region can provide pumping for methanol masers. In the colliding wind binary model context maser variability is attributed to seed photon modulation. Hence, future H ii models matching our observations could test predictions of these models in terms of the variability profiles of the $\rm {1.6 \, \rm {GHz}}$$\rm {OH}$ and $\rm {6.7 \, \rm {GHz} }$ methanol masers.
DNA polymerase zeta can efficiently replicate structures formed by AT/TA repeat sequences and prevent their deletion
Authors: Das Mili , Hile Suzanne E , Brewster Jennifer , Boer Jan Leendert , Bezalel-Buch Rachel , Guo Qiong , Yang Wei , Burgers Peter M , Eckert Kristin A , Freudenreich Catherine H 
Published: December 2024

Abstract
Long AT repeat tracts form non-B DNA structures that stall DNA replication and cause chromosomal breakage. AT repeats are abundant in human common fragile sites (CFSs), genomic regions that undergo breakage under replication stress. Using an in vivo yeast model system containing AT-rich repetitive elements from human CFS FRA16D, we find that DNA polymerase zeta (Pol ζ) is required to prevent breakage and subsequent deletions at hairpin and cruciform forming (AT/TA)n sequences, with little to no role at an (A/T)28 repeat or a control non-structure forming sequence. DNA polymerase eta is not protective for deletions at AT-rich structures, while DNA polymerase delta is protective, but not in a repeat-specific manner. Using purified replicative holoenzymes in vitro, we show that hairpin structures are most inhibitory to yeast DNA polymerase epsilon, whereas yeast and human Pol ζ efficiently synthesize these regions in a stepwise manner. A requirement for the Rev1 protein and the modifiable lysine 164 of proliferating cell nuclear antigen to prevent deletions at AT/TA repeats suggests a mechanism for Pol ζ recruitment. Our results reveal a novel role for Pol ζ in replicating through AT-rich hairpins and suggest a role for Pol ζ in rescue of stalled replication forks caused by DNA structures.
Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia
Authors: Pujar Abhinav , Pathania Amit , Hopper Corbin , Pandi Amir , Calderón Cristian Ruiz , Függer Matthias , Nowak Thomas , Kushwaha Manish 
Published: December 2024

Abstract
Coordinated actions of cells in microbial communities and multicellular organisms enable them to perform complex tasks otherwise difficult for single cells. This has inspired biological engineers to build cellular consortia for larger circuits with improved functionalities while implementing communication systems for coordination among cells. Here, we investigate the signalling dynamics of a phage-mediated synthetic DNA messaging system and couple it with CRISPR interference to build distributed circuits that perform logic gate operations in multicellular bacterial consortia. We find that growth phases of both sender and receiver cells, as well as resource competition between them, shape communication outcomes. Leveraging the easy programmability of DNA messages, we build eight orthogonal signals and demonstrate that intercellular CRISPRi (i-CRISPRi) regulates gene expression across cells. Finally, we multiplex the i-CRISPRi system to implement several multicellular logic gates that involve up to seven cells and take up to three inputs simultaneously, with single- and dual-rail encoding: NOT, YES, AND and AND-AND-NOT. The communication system developed here lays the groundwork for implementing complex biological circuits in engineered bacterial communities, using phage signals for communication.
PerR functions as a redox-sensing transcription factor regulating metal homeostasis in the thermoacidophilic archaeon Saccharolobus islandicus REY15A
Authors: Zhang Xuemei , Wu Pengju , Bai Ruining , Gan Qi , Yang Yunfeng , Li Haodun , Ni Jinfeng , Huang Qihong , Shen Yulong 
Published: December 2024

Abstract
Thermoacidophilic archaea thrive in environments with high temperatures and low pH where cells are prone to severe oxidative stress due to elevated levels of reactive oxygen species (ROS). While the oxidative stress responses have been extensively studied in bacteria and eukaryotes, the mechanisms in archaea remain largely unexplored. Here, using a multidisciplinary approach, we reveal that SisPerR, the homolog of bacterial PerR in Saccharolobus islandicus REY15A, is responsible for ROS response of transcriptional regulation. We show that with H2O2 treatment and sisperR deletion, expression of genes encoding proteins predicted to be involved in cellular metal ion homeostasis regulation, Dps, NirD, VIT1/CCC1 and MntH, is significantly upregulated, while expression of ROS-scavenging enzymes remains unaffected. Conversely, the expression of these genes is repressed when SisPerR is overexpressed. Notably, the genes coding for Dps, NirD and MntH are direct targets of SisPerR. Moreover, we identified three novel residues critical for ferrous ion binding and one novel residue for zinc ion binding. In summary, this study has established that SisPerR is a repressive redox-sensing transcription factor regulating intracellular metal ion homeostasis in Sa. islandicus for oxidative stress defense. These findings have shed new light on our understanding of microbial adaptation to extreme environmental conditions.
The ATPase activity of yeast chromosome axis protein Hop1 affects the frequency of meiotic crossovers
Authors: Dhyani Kshitiza M , Dash Suman , Joshi Sameer , Garg Aditi , Pal Debnath , Nishant Koodali T , Muniyappa Kalappa 
Published: December 2024

Abstract
Saccharomyces cerevisiae meiosis-specific Hop1, a structural constituent of the synaptonemal complex, also facilitates the formation of programmed DNA double-strand breaks and the pairing of homologous chromosomes. Here, we reveal a serendipitous discovery that Hop1 possesses robust DNA-independent ATPase activity, although it lacks recognizable sequence motifs required for ATP binding and hydrolysis. By leveraging molecular docking combined with molecular dynamics simulations and biochemical assays, we identified an ensemble of five amino acid residues in Hop1 that could potentially participate in ATP-binding and hydrolysis. Consistent with this premise, we found that Hop1 binds to ATP and that substitution of amino acid residues in the putative ATP-binding site significantly impaired its ATPase activity, suggesting that this activity is intrinsic to Hop1. Notably, K65A and N67Q substitutions in the Hop1 N-terminal HORMA domain synergistically abolished its ATPase activity, noticeably impaired its DNA-binding affinity and reduced its association with meiotic chromosomes, while enhancing the frequency of meiotic crossovers (COs). Overall, our study establishes Hop1 as a DNA-independent ATPase and reveals a potential biological function for its ATPase activity in the regulation of meiotic CO frequency.
Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits
Authors: Wan Jing , van Ouwerkerk Antoinette , Mouren Jean-Christophe , Heredia Carla , Pradel Lydie , Ballester Benoit , Andrau Jean-Christophe , Spicuglia Salvatore 
Published: December 2024

Abstract
There is growing evidence that a wide range of human diseases and physiological traits are influenced by genetic variation of cis-regulatory elements. We and others have shown that a subset of promoter elements, termed Epromoters, also function as enhancer regulators of distal genes. This opens a paradigm in the study of regulatory variants, as single nucleotide polymorphisms (SNPs) within Epromoters might influence the expression of several (distal) genes at the same time, which could disentangle the identification of disease-associated genes. Here, we built a comprehensive resource of human Epromoters using newly generated and publicly available high-throughput reporter assays. We showed that Epromoters display intrinsic and epigenetic features that distinguish them from typical promoters. By integrating Genome-Wide Association Studies (GWAS), expression Quantitative Trait Loci (eQTLs) and 3D chromatin interactions, we found that regulatory variants at Epromoters are concurrently associated with more disease and physiological traits, as compared with typical promoters. To dissect the regulatory impact of Epromoter variants, we evaluated their impact on regulatory activity by analyzing allelic-specific high-throughput reporter assays and provided reliable examples of pleiotropic Epromoters. In summary, our study represents a comprehensive resource of regulatory variants supporting the pleiotropic role of Epromoters.
Patients with membranous lupus nephritis form two clusters with different prognoses
Authors: Wang Zhipeng , Xiang Wang , Wang Yiqin , Yu Jianwen , Wang Xin , Ye Hongjian , Wu Haishan , Tang Ruihan , Xia Xi , Chen Wei 
Published: December 2024

ABSTRACT

Background and hypothesis
Membranous lupus nephritis (MLN) traditionally includes class V (alone), and may be associated with other classes (III or IV). The clinical, therapeutic, and prognostic relevance of the classification remains controversial.

Methods
A retrospective cohort of 412 MLN patients from the First Affiliated Hospital of Sun-Yat Sen University was followed for a median of 65.68 (interquartile range 23.13–131.70) months. The primary outcomes were adverse renal events including all-cause death and ESRD. Phenotypes were identified and validated using unsupervised clustering analysis (K-means), principal component analysis and decision tree analysis.

Results
Distinct clinical and pathological differences were noted between the traditional class IV + V and classes V + III and V, while class V + III and class V exhibited high similarities in clinical features and prognosis (P = 0.074). K-means clustering revealed high-risk (n = 180) and low-risk (n = 232) groups, with significant differences in adverse renal outcomes (9.2% vs 4.1%, P &lt; 0.001). To recognize the high-risk profile of MLN patients, a decision tree based on Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) score, hemoglobin, serum creatinine, traditional classification, and activity index of renal biopsy accurately clustered patients in the development (95.8% accuracy) and validation (87.1% accuracy) cohorts.

Conclusions
Two novel phenotypic clusters, more predictive than traditional classifications, enhance high-risk profile identification and prognostic accuracy.
Identifying the sources of mercury exposure in dental workers
Authors: Chuthong W , Trakulsrichai S , Sirinara P 
Published: December 2024

Summary
Dental professionals who handle dental amalgam are at risk of mercury exposure, though the prevalence and severity of elevated mercury levels from non-occupational sources are not well characterized. We report two dental workers who had elevated urinary mercury levels (37 and 25.6 mcg/L) during routine health screenings. Their previous mercury tests were normal, and no symptoms or abnormal findings were identified on clinical examination. Mercury exposure in these two workers occurred both occupationally through amalgam contact and non-occupationally via unregulated facial creams and seafood consumption. Their urine mercury levels normalized within 2 months after transitioning to amalgam-free roles and discontinuing the use of the facial products. No chelation or medication was administered in these cases. The identified primary source was inorganic mercury from unregistered facial creams, with levels measuring 18 302.17 and 6221.53 mcg/g surpassing the Thai regulation’s maximum limit of zero.