bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘Girls are Wanted More Than Men’: A Gendered Experience of Child Migration in the Mid-Nineteenth Century
Authors: Southart Jillian 
Published: August 2024

Abstract
On Christmas Day 1848 the Ramillies left England bound for Port Adelaide, Australia, carrying amongst its passengers a group of girls from London’s ragged schools and Marylebone Workhouse. An incidence of brutal punishment to which some of the girls were subjected on board ship went unreported in the British press at the time but became the subject of a heated debate in Parliament 12 months later. Through an examination of letters, press reports and official records, this article uses the journey of this one ship as a case study to illustrate the range of experiences, both negative and positive, faced by young poor female emigrants and demonstrates the ways in which those experiences were shaped by gender. It explores why emigration was seen as a particularly appropriate solution to the ‘problem’ of destitute girls and why the process itself was more challenging for them than for boys, using this analysis as a tool to bring into sharper focus some of the prevailing attitudes towards poor young women in the mid-nineteenth century. Finally, it shows how, whereas young women in similar situations are often portrayed as victims, some could, albeit operating within a restricted range of options, exercise at least some degree of choice. Early emigration schemes like this, operated by the Ragged School Union and others, have rarely figured in the historiography; this article will build on existing scholarship in gender, childhood and emigration studies and offer new insights into the life experiences of pauper girls in the mid-nineteenth century.
Music as incarnated beauty in J.R.R. Tolkien’s The Silmarillion: a neoplatonic reading
Authors: Fishley Daniel 
Published: August 2024

Abstract
In this study I examine key conceptual parallels between J.R.R. Tolkien’s literary imagination and a Neoplatonic mythopoetic. Specifically, I discuss how Tolkien’s Silmarillion deploys a transcendental conception of Beauty that, I argue, suggests similarities with the notion of Beauty discussed by Plotinus in his Enneads. Following the scholarship of Lisa Coutras (2016) and Michael John Halsall (2020), this study analyzes key sections from Tolkien’s work to demonstrate a Neoplatonic influence. This influence, I argue, is best understood via an incarnational logic that understands musical harmony and tonal beauty to be signs that signal an ultimate transcendent source in Tolkien’s legendarium. Falling short of arguing for a direct influence of the Neoplatonic tradition on Tolkien, this study seeks to demonstrate only a plausible link between Neoplatonic sources and Tolkien’s work.
X-ray AGNs with SRG/eROSITA: multiwavelength observations reveal merger triggering and post-coalescence circumnuclear blowout
Authors: Bickley Robert W , Ellison Sara L , Salvato Mara , Salim Samir , Patton David R , Merloni Andrea , Byrne-Mamahit Shoshannah , Ferreira Leonardo , Wilkinson Scott 
Published: August 2024

ABSTRACT
Major mergers between galaxies are predicted to fuel their central supermassive black holes (SMBHs), particularly after coalescence. However, determining the prevalence of active galactic nuclei (AGNs) in mergers remains a challenge, because AGN diagnostics are sensitive to details of the central structure (e.g. nuclear gas clouds, geometry, and orientation of a dusty torus) that are partly decoupled from SMBH accretion. X-rays, expected to be ubiquitous among accreting systems, are detectable through non-Compton-thick screens of obscuring material, and thus offer the potential for a more complete assessment of AGNs in mergers. But extant statistical X-ray studies of AGNs in mergers have been limited by either sparse, heterogeneous, or shallow on-sky coverage. We use new X-ray observations from the first SRG/eROSITA all-sky data release to characterize the incidence, luminosity, and observability of AGNs in mergers. Combining machine learning and visual classification, we identify 923 post-mergers in Dark Energy Camera Legacy Survey (DECaLS) imaging and select 4565 interacting galaxy pairs (with separations &lt;120 kpc and mass ratios within 1:10) from the Sloan Digital Sky Survey. We find that galaxies with X-ray AGNs are 2.0$\pm$0.24 times as likely to be identified as post-mergers compared to non-AGN controls, and that post-mergers are 1.8$\pm$0.1 times as likely to host an X-ray AGN as non-interacting controls. A multiwavelength census of X-ray, optical, and mid-IR-selected AGNs suggests a picture wherein the underlying AGN fraction increases during pair-phase interactions, that galaxy pairs within ~20 kpc become heavily obscured, and that the obscuration often clears post-coalescence.
Action-based dynamical models of M31-like galaxies
Authors: Gherghinescu Paula , Das Payel , Grand Robert J J , Orkney Matthew D A 
Published: August 2024

ABSTRACT
In this work, we present an action-based dynamical equilibrium model to constrain the phase-space distribution of stars in the stellar halo, present-day dark matter distribution, and the total mass distribution in M31-like galaxies. The model comprises a three-component gravitational potential (stellar bulge, stellar disc, and a dark matter halo), and a double power-law distribution function (DF), $f(\mathbf {J})$, which is a function of actions. A Bayesian model-fitting algorithm was implemented that enabled both parameters of the potential and DF to be explored. After testing the model-fitting algorithm on mock data drawn from the model itself, it was applied to a set of three M31-like haloes from the Auriga simulations (Auriga 21, Auriga 23, and Auriga 24). Furthermore, we tested the equilibrium assumption and the ability of a double power-law DF to represent the stellar halo stars. The model incurs an error in the total enclosed mass of around 10 per cent out to 100 kpc, thus justifying the equilibrium assumption. Furthermore, the double power-law DF used proves to be an appropriate description of the investigated M31-like haloes. The anisotropy profiles of the haloes were also investigated and discussed from a merger history point of view, however, our approach underscores to capture the non-equilibrium anisotropy information of stellar haloes in Auriga models, which is expected.
Constraining modified gravity with weak-lensing peaks
Authors: Davies Christopher T , Harnois-Déraps Joachim , Li Baojiu , Giblin Benjamin , Hernández-Aguayo César , Paillas Enrique 
Published: August 2024

ABSTRACTIt is well established that maximizing the information extracted from upcoming and ongoing stage-IV weak-lensing surveys requires higher order summary statistics that complement the standard two-point statistics. In this work, we focus on weak-lensing peak statistics to test two popular modified gravity models, $f(R)$ and nDGP, using the forge and bridge weak-lensing simulations, respectively. From these simulations, we measure the peak statistics as a function of both cosmological and modified gravity parameters simultaneously. Our findings indicate that the peak abundance is sensitive to the strength of modified gravity, while the peak two-point correlation function is sensitive to the nature of the screening mechanism in a modified gravity model. We combine these simulated statistics with a Gaussian Process Regression emulator and a Gaussian likelihood to generate stage-IV forecast posterior distributions for the modified gravity models. We demonstrate that, assuming small scales can be correctly modelled, peak statistics can be used to distinguish general relativity from $f(R)$ and nDGP models at the 2σ level with a stage-IV survey area of $300$ and $1000 \, \rm {deg}^2$, respectively. Finally, we show that peak statistics can constrain $\log _{10}\left(|f_{R0}|\right) = -6$ per cent to 2 per cent precision, and $\log _{10}(H_0 r_c) = 0.5$ per cent to 25 per cent precision.
GA-NIFS: the interplay between merger, star formation, and chemical enrichment in MACS1149-JD1 at z = 9.11 with JWST/NIRSpec
Authors: Marconcini C , D’Eugenio F , Maiolino R , Arribas S , Bunker A , Carniani S , Charlot S , Perna M , Rodríguez Del Pino B , Übler H , Willott C J , Böker T , Cresci G , Curti M , Jones G C , Lamperti I , Parlanti E , Venturi G 
Published: August 2024

ABSTRACT
We present JWST/NIRSpec integral-field spectroscopy observations of the z $\sim$ 9.11 lensed galaxy MACS1149-JD1, as part of the GA-NIFS programme. The data were obtained with both the G395H grating (R $\sim$ 2700) and the prism (R $\sim$ 100). This target shows a main elongated UV-bright clump and a secondary component detected in continuum emission at a projected distance of 2 kpc. The R2700 data trace the ionized-gas morpho-kinematics in between the two components, showing an elongated emission mainly traced by [O iii] $\lambda$5007. We spatially resolve [O ii] $\lambda \lambda $3726,3729, [O iii] $\lambda \lambda$4959,5007, and [O iii] $\lambda$4363, which enable us to map the electron density (n$_{\rm e} \sim 1.0 \times 10^3$ cm$^{-3}$), temperature (T$_{\rm e} \sim 1.6 \times 10^4$ K), and direct-method gas-phase metallicity (−1.2 to −0.7 dex solar). A spatially resolved full-spectrum modelling of the prism indicates a north-south gas metallicity and stellar age gradient between the two components. We found 3$\sigma$ evidence of a spatially resolved anticorrelation of the gas-phase metallicity and the star formation rate density, which is likely driven by gas inflows, enhancing the star formation in JD1. We employ high-z sensitive diagnostic diagrams to rule out the presence of a strong AGN in the main component. These findings show the unambiguous presence of two distinct stellar populations, with the majority of the mass ascribed to an old star formation burst, as suggested by previous works. We disfavour the possibility of a rotating-disc nature for MACS1149-JD1; we favour a merger event that has led to a recent burst of star formation in two separate regions, as supported by high values of [O iii] $\lambda$5007/$\mathrm{H}\,\beta$, ionized gas velocity dispersion, and gas-phase metallicity.
Y-switch: a spring-loaded synthetic gene switch for robust DNA/RNA signal amplification and detection
Authors: Gupta Krishna , Krieg Elisha 
Published: August 2024

Abstract
Nucleic acid tests (NATs) are essential for biomedical diagnostics. Traditional NATs, often complex and expensive, have prompted the exploration of toehold-mediated strand displacement (TMSD) circuits as an economical alternative. However, the wide application of TMSD-based reactions is limited by ‘leakage’—the spurious activation of the reaction leading to high background signals and false positives. Here, we introduce the Y-Switch, a new TMSD cascade design that recognizes a custom nucleic acid input and generates an amplified output. The Y-Switch is based on a pair of thermodynamically spring-loaded DNA modules. The binding of a predefined nucleic acid target triggers an intermolecular reaction that activates a T7 promoter, leading to the perpetual transcription of a fluorescent aptamer that can be detected by a smartphone camera. The system is designed to permit the selective depletion of leakage byproducts to achieve high sensitivity and zero-background signal in the absence of the correct trigger. Using Zika virus (ZIKV)- and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived nucleic acid sequences, we show that the assay generates a reliable target-specific readout. Y-Switches detect native RNA under isothermal conditions without reverse transcription or pre-amplification, with a detection threshold as low as ∼200 attomole. The modularity of the assay allows easy re-programming for the detection of other targets by exchanging a single sequence domain. This work provides a low-complexity and high-fidelity synthetic biology tool for point-of-care diagnostics and for the construction of more complex biomolecular computations.
Improved sub-genomic RNA prediction with the ARTIC protocol
Authors: Baudeau Thomas , Sahlin Kristoffer 
Published: August 2024

Abstract
Viral subgenomic RNA (sgRNA) plays a major role in SARS-COV2’s replication, pathogenicity, and evolution. Recent sequencing protocols, such as the ARTIC protocol, have been established. However, due to the viral-specific biological processes, analyzing sgRNA through viral-specific read sequencing data is a computational challenge. Current methods rely on computational tools designed for eukaryote genomes, resulting in a gap in the tools designed specifically for sgRNA detection. To address this, we make two contributions. Firstly, we present sgENERATE, an evaluation pipeline to study the accuracy and efficacy of sgRNA detection tools using the popular ARTIC sequencing protocol. Using sgENERATE, we evaluate periscope, a recently introduced tool that detects sgRNA from ARTIC sequencing data. We find that periscope has biased predictions and high computational costs. Secondly, using the information produced from sgENERATE, we redesign the algorithm in periscope to use multiple references from canonical sgRNAs to mitigate alignment issues and improve sgRNA and non-canonical sgRNA detection. We evaluate periscope and our algorithm, periscope_multi, on simulated and biological sequencing datasets and demonstrate periscope_multi’s enhanced sgRNA detection accuracy. Our contribution advances tools for studying viral sgRNA, paving the way for more accurate and efficient analyses in the context of viral RNA discovery.
Sarbecovirus programmed ribosome frameshift RNA element folding studied by NMR spectroscopy and comparative analyses
Authors: Hernández-Marín María , Cantero-Camacho Ángel , Mena Ignacio , López-Núñez Sergio , García-Sastre Adolfo , Gallego José 
Published: August 2024

Abstract
The programmed ribosomal frameshift (PRF) region is found in the RNA genome of all coronaviruses and shifts the ribosome reading frame through formation of a three-stem pseudoknot structure, allowing the translation of essential viral proteins. Using NMR spectroscopy, comparative sequence analyses and functional assays we show that, in the absence of the ribosome, a 123-nucleotide sequence encompassing the PRF element of SARS-CoV-2 adopts a well-defined two-stem loop structure that is conserved in all SARS-like coronaviruses. In this conformation, the attenuator hairpin and slippery site nucleotides are exposed in the first stem-loop and two pseudoknot stems are present in the second stem-loop, separated by an 8-nucleotide bulge. Formation of the third pseudoknot stem depends on pairing between bulge nucleotides and base-paired nucleotides of the upstream stem-loop, as shown by a PRF construct where residues of the upstream stem were removed, which formed the pseudoknot structure and had increased frameshifting activity in a dual-luciferase assay. The base-pair switch driving PRF pseudoknot folding was found to be conserved in several human non-SARS coronaviruses. The collective results suggest that the frameshifting pseudoknot structure of these viruses only forms transiently in the presence of the translating ribosome. These findings clarify the frameshifting mechanism in coronaviruses and can have a beneficial impact on antiviral drug discovery.
Direct nanopore RNA sequencing of umbra-like virus-infected plants reveals long non-coding RNAs, specific cleavage sites, D-RNAs, foldback RNAs, and temporal- and tissue-specific profiles
Authors: Johnson Philip Z , Needham Jason M , Lim Natalie K , Simon Anne E 
Published: August 2024

Abstract
The traditional view of plus (+)-strand RNA virus transcriptomes is that infected cells contain a limited variety of viral RNAs, such as full-length (+)-strand genomic RNA(s), (–)-strand replication intermediate(s), 3′ co-terminal subgenomic RNA(s), and viral recombinant defective (D)-RNAs. To ascertain the full complement of viral RNAs associated with the simplest plant viruses, long-read direct RNA nanopore sequencing was used to perform transcriptomic analyses of two related umbra-like viruses: citrus yellow vein-associated virus (CY1) from citrus and CY2 from hemp. Analysis of different timepoints/tissues in CY1- and CY2-infected Nicotiana benthamiana plants and CY2-infected hemp revealed: (i) three 5′ co-terminal RNAs of 281 nt, 442 nt and 671 nt, each generated by a different mechanism; (ii) D-RNA populations containing the 671 fragment at their 5′ends; (iii) many full-length genomic RNAs and D-RNAs with identical 3′end 61 nt truncations; (iv) virtually all (–)-strand reads missing 3 nt at their 3′ termini; (v) (±) foldback RNAs comprising about one-third of all (–)-strand reads and (vi) a higher proportion of full-length gRNAs in roots than in leaves, suggesting that roots may be functioning as a gRNA reservoir. These findings suggest that viral transcriptomes are much more complex than previously thought.
Oligodendroglioma patient survival is associated with circulating B-cells and age
Authors: Taylor Jennie W , Warrier Gayathri , Hansen Helen M , McCoy Lucie , Rice Terri , Guerra Geno , Francis Stephen S , Clarke Jennifer L , Bracci Paige M , Hadad Sara , Kelsey Karl T , Wrensch Margaret , Molinaro Annette M , Wiencke John K 
Published: August 2024

Abstract

Background
Variations in survival among patients with oligodendroglioma are unexplained by known prognostic factors. To assess the impact of peripheral immune profiles on prognosis, we applied immunomethylomics analyses—DNA methylation of archived whole blood samples, to characterize immune cells.

Methods
We compared the proportions of immune cells from patients with oligodendroglioma to other glioma subtypes and controls. We used recursive partitioning analysis (RPA) within the oligodendrogliomas to correlate with survival.

Results
Patients with oligodendrogliomas (141) were median age at diagnosis of 44 years; 57% male; 75% White; 60% prior chemotherapy; and 25% on dexamethasone at sample collection. Patients with oligodendrogliomas had immune profiles more similar to controls than other glioma subtypes, though with notably lower B-cells. RPA of patients with oligodendrogliomas delineated 2 survival groups based on an interaction between age and B-naïve cells. Patients with longer survival (median 24.2 years) were ≤42 years of age with higher B-naïve cells versus worse survival (median 16.9 years) who were ≤42 years of age with lower B-naïve cells or &gt;42 years of age (P = .00032). Patients with worse survival also had lower CD4- and CD8-naïve T-cells. Similar immune profiles were observed in an independent cohort of oligodendroglioma patients prior to surgery.

Conclusions
Peripheral blood immune profiles in oligodendroglioma suggested that younger patients with lower B-naïve cells experienced shorter survival. Though our findings lack of validation cohort and use a heterogenous patient population, they suggest peripheral blood immune profiles may be prognostic for patients with glioma and warrant further investigation.
Epidemiology of Pediatric Astrovirus Gastroenteritis in a Nicaraguan Birth Cohort
Authors: Rubinstein Rebecca J , Gutiérrez Lester , Toval-Ruíz Christian , Hammond Kelli , Bode Lars , Vinjé Jan , Vilchez Samuel , Becker-Dreps Sylvia , Bucardo Filemón , Vielot Nadja A , Reyes Yaoska 
Published: August 2024

Abstract

Background
Astrovirus is a leading cause of acute gastroenteritis in children worldwide. However, few prospective studies have analyzed astrovirus in community-dwelling pediatric populations in low- and middle-income countries.

Methods
We assessed the incidence, risk factors, clinical characteristics, genotypes, viral coinfections, and time distribution of astrovirus gastroenteritis in 443 healthy Nicaraguan children born in 2017 to 2018 who were followed for 36 months. Children were recruited from hospitals and birth records in an economically diverse neighborhood of León city. Astrovirus-positive episodes and genotypes were identified from stool with reverse transcription quantitative polymerase chain reaction and Sanger sequencing.

Results
Of 1708 total specimens tested, 80 children (18%) experienced at least 1 astrovirus episode, and 9 experienced repeat episodes, mostly during the rainy season (May–October). Initial astrovirus episodes were not associated with a lowered risk against future episodes. In exploratory analyses, home toilets were associated with a lower risk of future astrovirus episodes (hazard ratio, 0.19; 95% CI, .04–.91). Human astrovirus 5 episodes, representing 15% of all typed episodes, were associated with longer diarrhea and more symptomatic rotavirus coinfections.

Conclusions
Astrovirus was a common cause of gastroenteritis in this cohort, and future studies should clarify the role of astrovirus genotype in clinical infection severity.
Circulation of Non-falciparum Species in Niger: Implications for Malaria Diagnosis
Authors: Garba Mamane N , M. Moustapha Lamine , Sow Djiby , Karimoun Aichatou , Issa Ibrahima , Sanoussi Mamane K , Diallo Mamadou A , Doutchi Mahamadou , Diongue Khadim , Ibrahim Maman L , Ndiaye Daouda , Badiane Aida S 
Published: August 2024

Abstract

Background
Niger's National Malaria Control Programme and its partners use histidine-rich protein 2–based RDTs, which are specific to Plasmodium falciparum diagnosis. This study aimed to screen for the circulation of non-falciparum species in Zinder, a region of Niger, West Africa.

Methods
A cross-sectional study was carried out from July to December 2022 at the district hospital of the Zinder region of Niger. P falciparum histidine-rich protein 2–based rapid diagnostic tests were performed, and dried blood spot samples were collected for further laboratory multiplexed photo-induced electron transfer–polymerase chain reaction (PET-PCR) analysis on positive light microscopy from all patients with fever who attended the Zinder district hospital during the study period.

Results
In total, 340 dried blood spots were collected and analyzed by PET-PCR. Overall, 73.2% (95% CI, 68.2%–77.9%; 249/340) were positive for Plasmodium genus and species and represented the study population. Plasmodium species proportions were 89.5% (95% CI, 85.1%–93.1%; 223/249) for P falciparum, 38.5% (95% CI, 32.5%–44.9%; 96/249) for P malariae, 10.8% (95% CI, 7.3%–15.4%; 27/249) for P vivax, and 1.6% (95% CI, .4%–4.1%; 4/249) for P ovale. Single infection with Plasmodium species counted for 61.8% (95% CI, 55.5%–67.9%; 154/249), and the mixed infections rate, with at least 2 Plasmodium species, was 38.1% (95% CI, 32.1%–44.5%; 95/249). Single non-falciparum infections represented a rate of 10.0% (95% CI, 6.6%–14.5%; 25/249).

Conclusion
This study confirms the first evidence of Plasmodium vivax by PET-PCR in Niger in addition to the other 3 Plasmodium species. These findings underline the need to adapt malaria diagnostic tools and therapeutic management, as well as the training of microscopists, for recognition of non-falciparum plasmodial species circulating in the country. This will better inform the strategies toward malaria control and elimination, as well as the decision making of the health authorities of Niger.