bluuebunny/crossref_metadata_2025 huggingface dataset:
A social constructivist viewpoint of media effects: extending the social influence model of technology use to media effects
Authors: Wolfers Lara N
Published: August 2024

New media technologies are often assumed to have negative effects on user’s mental health. However, several studies found no or only small effects. Building on a social constructivist perspective on media effects, this article aims to advance the debate around media’s effect on mental health, theoretically by proposing an extension of the social influence model of technology use. Mirroring the original model’s argumentation for media characteristics, the proposed extension assumes that there is a conceptual difference between perceived and objective media use and that in addition to objective media use, also media use perceptions influence users’ mental health. Finally, it is assumed that media use perceptions are socially constructed, meaning that the social environment influences how an individual perceives their own media use. Previous research supporting the model’s assumption as well as open questions requiring more research are discussed.
Right ventricular function in Marfan patients remains stable despite multiple cardiac interventions
Authors: Mihalj Maks , Nucera Maria , Ferro Cyril , Mosbahi Selim , Haynes Alan , Yildiz Murat , Heinisch Paul Philipp , Schoenhoff Florian S
Published: August 2024

OBJECTIVES

Mitral valve regurgitation and left ventricular dysfunction are cardiovascular symptoms of Marfan syndrome. There is a paucity of information on tricuspid valve regurgitation and right ventricular function. In patients with Marfan syndrome, we looked at long-term changes in right ventricular function, tricuspid valve regurgitation and freedom from tricuspid valve repair.

METHODS

Retrospective-observational single-centre analysis on right ventricular function and tricuspid regurgitation in Marfan patients who underwent surgery with cardioplegic arrest between 1995 and 2020. Patients were followed-up from 1st operation until death, with echocardiographic changes analysed longitudinally. Composite end point was tricuspid annular plane systolic excursion (TAPSE) ≤16 mm, severe tricuspid regurgitation or tricuspid repair.

RESULTS

The study included 135 patients who underwent 193 operations, 58 of those were reoperations in 40 patients. Median age at 1st operation was 35 years [interquartile range (IQR) 26–46], median follow-up was 8.0 years (IQR 3.0–16.0) and median time to 1st reoperation was 7.5 years (IQR 3.4–12.5). The composite end point occurred in 81 observations in 40 patients, mostly as a recurrent event, after median 7.0 years (IQR 1.0–13.0). Ten-year cumulative incidence for composite end point was 22.0% (95% CI 15–31) and 9.0% (95% CI 4.4–16) for new-onset TAPSE ≤16 mm, but no significant change in TAPSE was observed at 10 years. Tricuspid regurgitation was associated with increased risk of annual progression (P < 0.001), but not clinically relevant at 10 years. Actuarial 10-year survival was 91.1%.

CONCLUSIONS

In Marfan patients with a history of cardiac surgery and subsequent reoperations, the right ventricular function remains stable. The incidence of severe tricuspid regurgitation and tricuspid repair remain low.
Germline mutation rate predicts cancer mortality across 37 vertebrate species
Authors: Kapsetaki Stefania E , Compton Zachary T , Mellon Walker , Vincze Orsolya , Giraudeau Mathieu , Harrison Tara M , Abegglen Lisa M , Boddy Amy M , Maley Carlo C , Schiffman Joshua D
Published: August 2024

Background and objectives

Cancer develops across nearly every species. However, cancer occurs at unexpected and widely different rates throughout the animal kingdom. The reason for this variation in cancer susceptibility remains an area of intense investigation. Cancer evolves in part through the accumulation of mutations, and therefore, we hypothesized that germline mutation rates would be associated with cancer prevalence and mortality across species.

Methodology

We collected previously published data on germline mutation rate and cancer mortality data for 37 vertebrate species.

Results

Germline mutation rate was positively correlated with cancer mortality (P-value = 0.0008; R2 = 0.13). Controlling for species’ average parental age, maximum longevity, adult body mass or domestication did not improve the model fit (the change (Δ) in Akaike Information Criterion (AIC) was less than 2). However, this model fit was better than a model controlling for species trophic level (ΔAIC > 2).

Conclusions and implications

The increased death rate from cancer in animals with increased germline mutation rates may suggest underlying hereditary cancer predisposition syndromes similar to those diagnosed in human patients. Species with higher germline mutation rates may benefit from close monitoring for tumors due to increased genetic risk for cancer development. Early diagnoses of cancer in these species may increase their chances of overall survival, especially for threatened and endangered species.
Clinical impact of atrial fibrillation progression in patients with heart failure with preserved ejection fraction: A report from the CHART-2 Study
Authors: Ito Tomohiro , Noda Takashi , Nochioka Kotaro , Shiroto Takashi , Yamamoto Nobuhiko , Sato Hiroyuki , Chiba Takahiko , Hasebe Yuhi , Nakano Makoto , Takahama Hiroyuki , Takahashi Jun , Miyata Satoshi , Shimokawa Hiroaki , Yasuda Satoshi
Published: August 2024

Aims

Atrial fibrillation (AF) frequently coexists with heart failure with preserved ejection fraction (HFpEF), and clinical outcomes of patients with AF vary depending on its subtype. While AF progression characterized by the transition from paroxysmal AF to persistent AF is sometimes observed, the incidence and clinical impact of AF progression in patients with HFpEF remain to be explored.

Methods and results

We enrolled patients with HFpEF and paroxysmal AF from the Chronic Heart Failure Analysis and Registry in the Tohoku District-2 (CHART-2) Study. AF progression was defined as the transition from paroxysmal AF to persistent AF. A total of 718 patients (median age: 72 years, 36% were female) were enrolled. For a median follow-up of 6.0 years (interquartile range: 3.0–10.2 years), AF progression occurred in 105 patients (14.6%), with a cumulative incidence of 16.7% at 10 years. In the multivariable Cox proportional hazards model, previous hospitalization for heart failure [hazard ratio (HR) 1.74, 95% confidence interval (CI) 1.16–2.60; P = 0.007] and left atrial diameter (per 5-mm increase) (HR 1.37, 95% CI 1.20–1.55; P < 0.001) were significantly associated with AF progression. Furthermore, AF progression was significantly linked to worsening heart failure (adjusted HR 1.68, 95% CI 1.18–2.40; P = 0.004). Notably, 27 cases (26%) of worsening heart failure occurred within 1 year following AF progression.

Conclusion

In patients with HFpEF, AF progression is significantly associated with adverse outcomes, particularly worsening heart failure. An increased risk is observed in the early phases following progression to persistent AF.

Registration

Clinical Trials.gov Identifier: NCT00418041
Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss
Authors: Klirs Yael , Novosolov Maria , Gissi Carmela , Garić Rade , Pupko Tal , Stach Thomas , Huchon Dorothée
Published: August 2024

Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined.
Efficient implementation of equivalent medium parametrization in finite-difference seismic wave simulation methods
Authors: Jiang Luqian , Zhang Wei
Published: August 2024

Gridpoint discretization of the model has a significant impact on the accuracy of finite-difference seismic waveform simulations. Discretizing the discontinuous velocity model using local point medium parameters can lead to artefact diffraction caused by the stair-step representation and inaccuracies in calculated waveforms due to interface errors, particularly evident when employing coarse grids. To accurately represent model interfaces and reduce interface errors in finite-difference calculations, various equivalent medium parametrization methods have been developed in recent years. Most of these methods require volume-integrated averaging calculations of the medium parameter values within grid cells. The simplest way to achieve this volume averaging is to apply numerical integration averaging to all grid cells. However, this approach demands considerable computational time. To address this computational challenge, we propose employing a set of auxiliary grids to identify which grid cells intersected by the welded interface and perform volume averaging only on these specific cells, thereby reducing unnecessary computational overhead. Additionally, we present a 3-D tilted transversely isotropic equivalent medium parametrization method, which effectively suppresses interface errors and artefact diffraction under the application of coarse grids. We also provide an approach for computing the normal direction of the interface, which is essential for the tilted transversely isotropic equivalent medium parametrization. Numerical tests validate the accuracy of the tilted transversely isotropic equivalent medium parametrization method and demonstrate the practicality of the implementation proposed in this paper for complex models.
Sexual health interventions with social marketing approach targeting young people: a scoping review
Authors: Putkonen Hanna , Kallio Hanna , Kylmä Jari , Rissanen Tiina , Sormunen Marjorita
Published: August 2024

In a fast-paced digital and global environment, sexual education must keep up with young people’s sexual health needs. Social marketing is an approach that has been used in sexual health promotion for young people. The objective of the scoping review is to identify and map the use of social marketing in sexual health promotion for young people. Specifically, the content, delivery methods and effects of interventions on sexual health were researched. Six databases were systemically searched to capture the relevant peer-reviewed quantitative, qualitative and mixed methods articles without time restrictions that provided evidence of sexual health-related social marketing interventions targeting young people aged 11–25. An inductive and deductive content analysis was performed. Nineteen studies were included in the data. The content of interventions was dominated by sexual risks and risk prevention, focusing particularly on sexually transmitted diseases, unwanted pregnancies and sexual violence. Additionally, interventions included topics of morals of sexual relationships and changes in the body. The delivery of interventions occurred through various media channels, events and activities, while the effects of interventions were monitored as improvements in sexual perceptions and sexual behaviour, limited gender-related effects, limited evidence of intervention attributed to behaviour and effects in different age groups. The social marketing approach was mostly preventive and concentrated on the risks, whereas the delivery methods were diverse and creative, combining modern and already well-established channels. Sexuality should be seen comprehensively, and interventions should respond to the full range of young people’s needs.
Dual β-lactams for the treatment of Mycobacterium abscessus: a review of the evidence and a call to act against an antibiotic nightmare
Authors: Longo Bianca Maria , Trunfio Mattia , Calcagno Andrea
Published: August 2024

Mycobacterium abscessus complex is a group of rapidly growing non-tuberculous mycobacteria (NTM), increasingly emerging as opportunistic pathogens. Current treatment options for these microorganisms are limited and associated with a high rate of treatment failure, toxicity and recurrence. In search of new therapeutic strategies, interest has grown in dual β-lactam (DBL) therapy, as research recently discovered that M. abscessus cell wall synthesis is mainly regulated by two types of enzymes (d,d-transpeptidases and l,d-transpeptidases) differently susceptible to inhibition by distinct β-lactams. In vitro studies testing several DBL combinations have shown synergy in extracellular broth cultures as well as in the intracellular setting: cefoxitin/imipenem, ceftaroline/imipenem, ceftazidime/ceftaroline and ceftazidime/imipenem. The addition of specific β-lactamase inhibitors (BLIs) targeting M. abscessus β-lactamase did not significantly enhance the activity of DBL combinations. However, in vivo data are lacking. We reviewed the literature on DBL/DBL-BLI-based therapies for M. abscessus infections to raise greater attention on this promising yet overlooked treatment option and to guide future preclinical and clinical studies.
A Validated LC-MS/MS Assay for the Quantification of Cholate Isotopes in Human Serum
Authors: Helmke Steve M , McRae Michael P , Christians Uwe , Shokati Touraj , Everson Gregory T
Published: August 2024

Background

Current methods for evaluating liver health rely on nonspecific blood tests, elastography surrogates for fibrosis, and invasive procedures, none of which directly measure liver function and physiology. Herein we present the analytical validation of a unique, highly sensitive LC-MS/MS assay and dual-sample oral (DuO) cholate challenge test to reliably quantify serial serum concentrations of cholate isotopes administered to patients with liver diseases. The clearance of administered cholate isotopes measured by the assay provides information about liver function and physiology.

Methods

Analytical method validation of the cholate assay analytes (endogenous unlabeled cholic acid, 24-13C-cholic acid, and 2,2,4,4-D4-cholic acid) in terms of accuracy, precision, analytical sensitivity, analytical specificity, and range of reliable response was completed in human serum samples spiked with quality controls and calibrators in accordance with applicable guidelines. DuO test parameters were validated using samples from 48 subjects representing various liver disease etiologies.

Results

Accuracy (mean biases) for all analytes ranged from 0.1% to 3.7%. Using a nested components-of-variance design (20 days, 2 runs per day, 2 replicates per sample), total imprecision for all analytes ranged from 2.3% to 8.4%. Lower and upper limits of quantitation were established and validated at 0.1 to 10.0 µM. Matrix effects and potential interferents did not affect assay performance. DuO test validation met all prespecified acceptance criteria.

Conclusions

The method validation studies described herein established the performance characteristics in terms of accuracy, precision, analytical sensitivity, analytical specificity, reportable ranges, and reference intervals of the LC-MS/MS cholate assay and DuO test.
Isolation and identification of entomopathogenic fungi strains for Colorado potato beetle (Leptinotarsa decemlineata) control
Authors: Konopická Jana , Skoková Habuštová Oxana , Jánová Nicole , Žurovcová Martina , Doležal Petr , Zemek Rostislav
Published: August 2024

Aims

The Colorado potato beetle, Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae) is the most widespread insect pest that causes major economic losses, especially on potatoes. Due to heavy insecticide use, this species now resists most pesticides, posing a significant control challenge. Frequent pesticide application also harms non-target organisms, the environment, and human health. Hence, utilizing biocontrol agents like entomopathogenic fungi (EPF) offers a viable alternative for pest management. The aim of this study was to identify and characterize new EPF strains isolated from soil samples and evaluate their efficacy against adult L. decemlineata under laboratory conditions.

Methods and results

Soil samples were collected in potato fields or uncultivated areas adjacent to the field in the Czech Republic and the EPF strains were isolated using a modified Tenebrio bait method. A total of 20 fungal strains were isolated and identified using morphological and molecular markers based on the 28S rRNA, ITS, and elongation factor 1-alpha gene sequences as Beauveria bassiana (Bals.-Criv.) Vuill., Beauveria brongniartii (Sacc.) Petch, and Cordyceps fumosorosea (Wize) Kepler, B. Shrestha & Spatafora (Hypocreales: Cordycipitaceae), Purpureocillium lilacinum (Thom.) Luangsa-ard, Houbraken, Hywel-Jones & Samson (Hypocreales: Ophiocordycipitaceae), Metarhizium brunneum (Petch), and Metarhizium robertsii Bisch., Rehner & Humber (Hypocreales: Clavicipitaceae). The bioassays revealed high variability among virulence of these strains against L. decemlineata with the shortest median time to death (LT50 = 5 days) in M. robertsii strain MAN3b.

Conclusions

Results shown that some EPF strains, particularly those of genera Metarhizium, can be promising biocontrol agents against the Colorado potato beetle.
Dietary manganese supplementation decreases hepatic lipid deposition by regulating gene expression and enzyme activity involved in lipid metabolism in the liver of broilers
Authors: Yang Ke , Cui Xiaoyan , Hu Yangyang , Feng Xinyu , Chen Wenpeng , Zhang Weiyun , Zhang Liyang , Li Sufen , Hu Yun , Li Tingting , Wang Shengchen , Luo Xugang
Published: August 2024

This study aimed to characterize the effects of different dietary forms of supplemental manganese (Mn) on hepatic lipid deposition, gene expression, and enzyme activity in liver fat metabolism in 42-d-old broiler chickens. In total 420 one-day-old Arbor Acres (AA) broilers (rooster:hen = 1:1) were assigned randomly based on body weight and sex to 1 of 6 treatments (10 replicate cages per treatment and 7 broilers per replicate cage) in a completely randomized design using a 2 (sex) × 3 (diet) factorial arrangement. The 3 diets were basal control diets without Mn supplementation and basal diets supplemented with either Mn sulfate or Mn proteinate. No sex × diet interactions were observed in any of the measured indexes; thus, the effect of diet alone was presented in this study. Dietary Mn supplementation increased Mn content in the plasma and liver, adipose triglyceride lipase (ATGL) activity, and ATGL mRNA and its protein expression in the liver by 5.3% to 24.0% (P < 0.05), but reduced plasma triglyceride (TG), total cholesterol, and low-density lipoprotein (LDL-C) levels, liver TG content, fatty acid synthase (FAS) and malic enzyme (ME) activities, mRNA expression of sterol-regulatory element-binding protein 1 (SREBP1), FAS, stearoyl-coA desaturase (SCD), and ME, as well as the protein expression of SREBP1 and SCD in the liver by 5.5% to 22.8% (P < 0.05). No differences were observed between the 2 Mn sources in all of the determined parameters. Therefore, it was concluded that dietary Mn supplementation, regardless of Mn source, decreased hepatic lipid accumulation in broilers by inhibiting SREBP1 and SCD expression, FAS and ME activities, and enhancing ATGL expression and activity.
The proper scope of education for flourishing
Authors: Kristjánsson Kristján , VanderWeele Tyler J
Published: August 2024

The concept of flourishing has recently come into vogue within various areas of the humanities and social sciences (e.g. philosophy, psychology, economics, health, education). This article focuses on its potential role within education, where the retrieval of flourishing has perhaps been most visible of all the recent areas of interest, setting in motion what some have called a ‘flourishing bandwagon’. This bandwagon has blazed a trail for the somewhat radical view that flourishing can be seen not only as a significant aim, but even the central aim, of all educational endeavours. Recent criticisms of the flourishing view focus on its potential vacuity and its unhelpful conflation of general and laudable, but uneducable, socio-political and psycho-moral aims with educable ones, hence placing unreasonable burdens on practitioners. After providing a brief historical and conceptual backdrop, this article aims at fleshing out and finessing the scope of education for flourishing and, hence at responding to the recent critics. This is done inter alia through an analogy with health where a similar theoretical problem beckons about possible conceptual underpopulations and overpopulations of the content of the aim of health itself.
Physicians’ opinions on the utilization of generic medications in Gulf Cooperation Council countries: a narrative review
Authors: Rafiq Rubina , Ooi Guat See , Sridhar Sathvik B , Ejaz Haris
Published: August 2024

Objective

This review paper explores strategies and recommendations for reducing healthcare expenses in the Gulf Cooperation Council (GCC) by understanding physicians’ attitudes regarding the utilization of generic medicines.

Methods

A comprehensive search of seven databases yielded 24 437 titles and abstracts. Using inclusion criteria focusing on physicians’ insights into generic prescribing and exclusion criteria, cutting out systematic reviews, case studies, and non-English articles, the review process led to an in-depth analysis of six studies.

Results

Findings revealed that while physicians generally comprehend terms like “generic”, “brand”, and “bioequivalence”, they face difficulty discussing bioequivalence with patients. Lack of emphasis on generic medicines in medical education and complex patient communication were potential impediments to generic medicine prescribing in the GCC countries. Strategies & Recommendations: Promoting the benefits of generic drugs could support their usage and help decrease healthcare costs. Improving medical education to include a larger focus on generic medications and their benefits, as well as training physicians in effectively communicating bioequivalence concepts to patients, could promote the use of more cost-effective, generic options.

Conclusion

The review calls for attention to the potential of generic medicine prescribing to reduce healthcare expenses in the GCC. Future research studies should consider broadening the geographical scope to provide global insights into these issues and their possible solutions.
Post-Artesunate Delayed Hemolysis in Pediatric Malaria Patients in the United States
Authors: Sundararaman Sesh A , Hanze Villavicencio Karen L , Roper Brianne , Wang Ziyi , Davis Amy K F , Mayhew Jonathan A , Wang Michelle L , Tang Nina L , Soma Vijaya L , Shust Gail F , Feeney Margaret E , Trehan Indi , Weatherhead Jill E , John Chandy C , Gerber Jeffrey S , Odom John Audrey R
Published: August 2024

Post-artesunate delayed hemolysis (PADH) occurred in 6 of 24 children treated with artesunate for severe malaria in the United States; however, severe hemolysis requiring hospitalization or transfusion was rare. In children in the United States treated with artesunate, counseling, and symptom monitoring may be preferred to weekly laboratory surveillance for PADH.
‘Girls are Wanted More Than Men’: A Gendered Experience of Child Migration in the Mid-Nineteenth Century
Authors: Southart Jillian
Published: August 2024

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

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

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 <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

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

It 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

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

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

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

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

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

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 >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

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

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.