bluuebunny/crossref_metadata_2025 huggingface dataset:
Delineating Care Recipient Burden Constructs: Development and Validation of the CARE-2B Scale for Care Recipient Self-Perceived Burden and Proxy Assessment of Caregiver Burden
Authors: Kuharic Maja , Mulhern Brendan , Sharp Lisa K , Turpin Robin S , Pickard A Simon
Published: October 2024

Background and Objectives

Care Recipient Self-Perceived Burden (CR-SPB) to Caregivers is an important but overlooked aspect within the caregiver-care recipient relationship. This study aimed to 1) develop and validate the CARE-2B (Care Recipient's Two Burden) Scale, assessing both CR-SPB and their proxy assessment of caregiver burden (Proxy-CB); 2) examine whether the CR-SPB and Proxy-CB differ from caregiver burden’s own assessment and other health and social care constructs.

Research Design and Methods

Data were collected from 504 caregiver-care recipient dyads in the US using an online panel between August 2022 and February 2023. Care recipients completed the CARE-2B Scale, which includes two subscales: their self-perceived burden (CR-SPB) and their proxy assessment of caregiver burden (Proxy-CB). Care recipients also completed measures related to health, well-being: SPB-scale, EQ-5D-5L, and EQ-HWB. Caregivers completed CarerQoL and ASCOT-Carer. Psychometric analysis included exploratory and confirmatory factor analysis, item response theory (IRT), and construct validity.

Results

CR-SPB correlated strongly with the SPB-Scale (r=0.73), while Proxy-CB correlated more strongly with caregiver-reported burden (r=0.61). Both CR-SPB and Proxy-CB items demonstrated good discrimination and information coverage in IRT analysis. EFA further supported the distinctiveness of CR-SPB and Proxy-CB, with CR-SPB items loading on a separate factor from caregiver burden and health constructs, while Proxy-CB aligned with caregiver-reported burden.

Discussion and Implications

The CARE-2B Scale innovatively assesses both CR-SPB and Proxy-CB from the care recipient's perspective, providing new insights into the caregiving relationship. This dual-perspective measure has implications for enhancing care strategies for individuals with chronic conditions or disabilities and their caregivers.
A real scale application of a novel set of spatial and similarity features for detection and classification of natural seismic sources from distributed acoustic sensing data
Authors: Huynh C , Hibert C , Jestin C , Malet J -P , Lanticq V
Published: October 2024

Distributed acoustic sensing (DAS) turns a fibre optic into a very dense network of equally distributed seismic sensors. We focused on the high-density sampling of the seismic wavefield, expressed in strain rates, measured by DAS. Classical approaches used to identify seismic signals rely on the recorded features at one station, but it is difficult to include spatial information in case of dense seismic station networks. This work aims at introducing new spatial and similarity features for seismic event classification suitable to analyse DAS observations. We propose a processing chain based on the XGBoost algorithm and the use of specifically designed spatiotemporal and similarity features for the event classification, and Markov random field for the spatial clustering. The methodology is designated to be applied on a continuous stream of DAS observations. We tested our processing chain to detect earthquakes and quarry blasts recorded in the region by permanent seismic networks and included in the RENASS catalogue. These events are part of a strain-rate seismic survey carried out during a 3 weeks campaign of DAS measurements along à 91 km fibre optic cable deployed in the central Pyrenees mountains (France). Despite the high anthropogenic activities along the fibre optic path, the proposed method succeeded in detecting earthquakes of magnitude >0.4 and quarry blasts of magnitude >1.0 while limiting the number of false alarms. This performance is particularly noteworthy for low-magnitude events, where detection is accomplished despite a lower signal-to-noise ratio compared to traditional seismometers. The methodology opens the door to real time detection and classification of seismic events measured with long-distance fibre optic systems.
Suitability of smoking cessation support from social and community service organizations: perspectives of Dutch clients
Authors: Visser Judith E M , Burger Judith , Rozema Andrea D , Kunst Anton E , Kuipers Mirte A G
Published: October 2024

Social and community service organizations (SCSOs) may be a promising new environment to more successfully reach people with a lower socioeconomic position (SEP) for smoking cessation support. However, studies that investigate clients’ perspectives of the suitability of SCSOs as a setting to discuss smoking are scarce. This study aimed to (i) investigate the suitability of smoking cessation support provided by SCSOs, according to people with a low SEP, and (ii) explore their reasons for considering it suitable or unsuitable. Semi-structured interviews were conducted with 19 individuals with a low SEP who smoked regularly (N = 14) or had smoked regularly (N = 5). They have been in contact with SCSOs in a specific neighborhood in Amsterdam. Data were analyzed using a thematic approach. Participants generally considered SCSOs as suitable for providing smoking cessation support, as professionals are involved, build a relationship of trust, and offer personalized and holistic support. SCSOs are located nearby and familiar, they provide support in both group and individual settings and might offer additional supportive (group)activities. A number of participants expressed doubts about the waiting time for support, the fact that the needed support might exceed professionals’ expertise, and the lack of aftercare. SCSOs can be an additional opportunity for providing smoking cessation support that aligns with the circumstances of lower SEP people. To harness the potential, smoking cessation could be integrated into education programs and training among professionals could be promoted. Policy changes within and outside SCSOs would be needed.
The Genocide Convention is “Our Cause”: International Women’s Advocacy for the Criminalization of Genocide, 1945–1952
Authors: Kimble Sara L
Published: October 2024

In 1948, the United Nations Convention on the Prevention and Punishment of the Crime of Genocide was official recognized under international law. Few, however, understand the role of international women’s rights organizations in the politics of the convention, the ratification process, and its application in the immediate postwar era. Rooted in their knowledge of Nazi atrocities and wartime activism, women’s organizations supported Raphael Lemkin’s campaign, but also critiqued the convention’s failure to address sexual violence and political repression of certain vulnerable groups. This article explores how women’s rights leaders supported the Genocide Convention as a crucial mechanism for preventing a repetition of atrocities, how they committed early on to applying the law to intervene and protect human rights, and how fissures later emerged between these various international women’s rights groups in the Cold War era.
Behavioral and neurophysiological signatures of cognitive control in humans and rats
Authors: Linton Samantha R , Lees Ty , Iturra-Mena Ann , Kangas Brian D , Nowicki Genevieve , Lobien Rachel , Vitaliano Gordana , Bergman Jack , Carlezon William A , Pizzagalli Diego A
Published: October 2024

Background

Deficits in cognitive control are implicated in numerous neuropsychiatric disorders. However, relevant pharmacological treatments are limited, likely due to weak translational validity of applicable preclinical models used. Neural indices derived from electroencephalography may prove useful in comparing and translating the effects of cognition-enhancing drugs between species. In the current study, we aimed to extend our previous cross-species results by examining if methylphenidate (MPH) modulates behavioral and neural indices of cognitive control in independent cohorts of humans and rats.

Methods

We measured continuous electroencephalography data from healthy adults (n = 25; 14 female) and Long Evans rats (n = 22; 8 female) and compared both stimulus- and response-locked event-related potentials and spectral power measures across species, and their MPH-related moderation following treatment with vehicle (placebo) or 1 of 2 doses of MPH.

Results

Across both species, linear mixed effects modeling confirmed the expected Flanker interference effect on behavior (eg, accuracy) and response-related event-related potentials. Unexpectedly, in contrast to past work, we did not observe any task-related effects on the spectral power of rodents. Moreover, MPH generally did not modulate cognitive control of either species, although some species-specific patterns offer insight for future research.

Conclusions

Collectively, these findings in independent human and rodent subjects replicate some of our previously reported behavioral and neurophysiological patterns partly consistent with the notion that similar neural mechanisms may regulate cognitive control in both species. Nonetheless, these results showcase an approach to accelerate translation using a coordinated between-species platform to evaluate pro-cognitive treatments.
Finitely Presented Kernels of Homomorphisms From Hyperbolic Groups Onto Free Abelian Groups
Authors: Kropholler Robert , Llosa Isenrich Claudio
Published: October 2024

For every $m\geq 2$ we produce an example of a non-hyperbolic finitely presented subgroup $H < G$ of a hyperbolic group $G$, which is the kernel of a surjective homomorphism $\phi : G\to{\mathbb Z}^{m}$. The examples we produce are of finiteness type $F_{2}$ and not $F_{3}$.
CpG-Adjuvanted Virus-like Particle Vaccine Induces Protective Immunity Against Leishmania donovani Infection
Authors: Yoon Keon-Woong , Chu Ki Back , Eom Gi-Deok , Mao Jie , Moon Eun-Kyung , Kim Sung Soo , Quan Fu-Shi
Published: October 2024

Visceral leishmaniasis poses a significant public health challenge due to the lack of an approved human vaccine. We attempted to enhance the efficacy of virus-like particle (VLP) vaccines expressing the Leishmania donovani promastigote surface antigen (LdPSA) by adjuvanting with CpG oligodeoxynucleotide. Here, we evaluated adjuvanted vaccine-induced immune responses and their efficacies in mice challenged with mCherry-expressing L donovani promastigotes. Adjuvanted LdPSA-VLP vaccination significantly elevated parasite-specific IgG serum antibody levels. Additionally, vaccinated mice exhibited enhanced germinal center B cells and splenic T-cell activities as compared with unimmunized mice. Importantly, adjuvanted LdPSA-VLPs reduced the levels of inflammatory cytokines interferon γ and interleukin 6 in visceral organs, leading to decreased total parasite burden and protection against L donovani challenge. Our findings indicate that CpG oligodeoxynucleotide enhanced the protection conferred by LdPSA-VLPs, offering a promising step toward effective visceral leishmaniasis vaccine development.
Differential frequency of persister cells in clinically derived isolates of Pseudomonas aeruginosa after exposure to cefiderocol and ceftolozane/tazobactam
Authors: Fouad Aliaa , Nicolau Samantha E , Tamma Pranita D , Simner Patricia J , Nicolau David P , Gill Christian M
Published: October 2024

Background

Bacterial persistence is a phenomenon whereby a subpopulation of bacteria survive high concentrations of an active antibiotic in the absence of phenotypic alterations. Persisters are associated with chronic and recurrent infections for pathogens including Pseudomonas aeruginosa. Understanding persister profiles of newer antibiotics such as cefiderocol and ceftolozane/tazobactam against P. aeruginosa is warranted as these agents generally target difficult-to-treat infections.

Methods

Persister formation was assessed using in vitro assays against nine clinical P. aeruginosa isolates exposed to cefiderocol or ceftolozane/tazobactam. Quantitative persister assays were performed using a stationary phase of bacteria challenged with 10-fold MIC drug concentrations. Persisters were quantitated as the percent persisters at 24 h and the log ratio (LR) difference in AUC for cfu for each antibiotic alone compared with growth control. The tolerance disc test (TDtest) was used to qualitatively detect persisters.

Results

Percent persisters at 24 h was lower with cefiderocol compared with ceftolozane/tazobactam for six of the nine tested isolates. Eight of the nine isolates had higher reduction in LR for cefiderocol groups, suggesting an overall higher and more rapid bacterial reduction in cefiderocol groups. For cefiderocol, five of the nine tested isolates lacked regrowth after replacement with glucose disc, suggesting no persistence via the TDtest. For ceftolozane/tazobactam, three isolates lacked persister formation.

Conclusions

Cefiderocol resulted in less bacterial persistence relative to ceftolozane/tazobactam against nine clinical P. aeruginosa isolates. Cefiderocol’s siderophore mechanism may be advantageous over ceftolozane/tazobactam through enhanced anti-persister effects. Clinical correlation of these findings is warranted as persisters can lead to antibiotic resistance and treatment failure.
Enhancing the volatile organic compound and biomass production by three biocontrol potential bacteria in corn steep liquor growth medium and development of cell freeze-drying process
Authors: Villanova Valeria , Andreolli Marco , Lampis Silvia , Panighel Annarita , Flamini Riccardo , Forte Vally , Zapparoli Giacomo
Published: October 2024

Aims

This study investigates the traits of three plant growth-promoting (PGP) and antagonistic bacteria, Pseudomonas protegens MP12, Bacillus sp. 3R4, and Bacillus sp. T22, to assess their potential application as biocontrol agents by using the ecofriendly and low-cost substrate Corn Steep Liquor (CSL) medium. Analyses of antagonism through volatile organic compounds (VOCs) production, biofilm formation, and growth performance were carried out.

Methods and results

Dual antagonism assay showed that all strains displayed significant antagonistic activity against Botrytis cinerea through VOCs. Gas chromatography demonstrated that strains in the CSL exhibited higher VOCs production than nutrient medium. Moreover, enhanced biofilm formation analysed by Calgary Biofilm Device, growth, and biomass were noted in CSL cultures. Pseudomonas protegens MP12, which showed higher cell concentration and biomass yield, was selected for freeze-drying treatments. Storage cell viability assays evidenced that it can be effectively preserved for nearly 7 months at 4°C.

Conclusion

The results here obtained showed that CLS medium enhanced VOCs production, biofilm formation, growth, and biomass of the antagonistic bacteria of the three strains. Eventually, the more effective strain P. protegens MP12 can be stored for nearly 7 months at 4°C.
Activation of the aryl hydrocarbon receptor via indole derivatives is a common feature in skin bacterial isolates
Authors: Elias Abigail E , McBain Andrew J , Aldehalan Faye A , Taylor George , O'Neill Catherine A
Published: October 2024

Aims

The aryl hydrocarbon receptor (AhR) is a ligand-activated receptor implicated in many inflammatory disorders. The skin microbiota plays a crucial role in maintaining epidermal barrier integrity and is thought to modulate skin homeostasis partly through the production of AhR ligands, including metabolites of microbial tryptophan metabolism such as indole derivatives. Here, we report the skin microbiota that activate AhR and their unique tryptophan metabolite profiles.

Methods and results

Of the bacteria isolated from healthy human skin and screened for the ability to metabolize tryptophan (18 species, five genera), 14 were positive. The tryptophan metabolites of 10 positive and two negative bacteria were then characterized using liquid chromatography-mass spectrometry. Whole genome sequencing confirmed the presence of key genes involved in the indole-3-pyruvic acid pathway within the genomes of indole-3-acetaldehyde, indole-3-acetic acid, and indole-3-aldehyde-producing organisms. A cell-based luciferase reporter gene assay identified functional agonist activity against human AhR in the culture supernatants of 12 of the 18 species tested. High indole derivative-producing organisms induced potent AhR activation.

Conclusions

These data demonstrate the relationship between skin microbiota, tryptophan metabolites, and AhR activation.
Hip geometry and strength remain stable the first year after kidney transplantation—an ibandronate/placebo post hoc analysis
Authors: Strømmen Ruth C , Godang Kristin , Hovd Markus H , Finnes Trine E , Smerud Knut , Hartmann Anders , Åsberg Anders , Bollerslev Jens , Pihlstrøm Hege K
Published: October 2024

The sensitivity of bone mineral density (BMD) to identify patients with high fracture risk after kidney transplantation is low, therefore alternative tools are needed. Hip Structure Analysis (HSA) provides an estimation of hip structural geometry and strength based on conventional DXA scans for hip analyses. We aimed to investigate the effect of antiresorptive therapy on hip geometrical and strength parameters by HSA. In a post hoc analysis of a 12-month randomized, double-blind, placebo-controlled trial evaluating the effect of ibandronate in addition to active vitamin D and calcium in kidney transplant recipients (KTR), we re-analyzed dual total hip and femoral neck DXA scans to measure cortical bone thickness (CBT) in the femoral neck (CBTNECK), calcar (CBTCALCAR), and shaft (CBTSHAFT), along with femur neck width, hip axis length, and to estimate buckling ratio and strength index. DXA measurements were performed within 5 weeks after transplantation and repeated at 10 weeks and 1-year post-transplant. The study included a total of 127 de novo KTR with estimated glomerular filtration rate >30 mL/min at baseline. The 5 geometrical and the strength and stability hip parameters remained stable over the first post-transplant year irrespective of antiresorptive therapy. We detected no statistically significant between-group differences in any of the HSA measures. Change in geometrical hip parameters and buckling ratio over the study duration was not correlated with change in plasma parathyroid hormone or change in dual total hip BMD. In this study, the so far largest of HSA in KTR, antiresorptive therapy with ibandronate for 12 months did not affect measures of hip geometry or strength.

Clinical Trial Registration: www.clinicaltrials.gov as NCT00423384, EudraCT number 2006-003884-30.
The evolution of thermal performance curves in fungi farmed by attine ant mutualists in above-ground or below-ground microclimates
Authors: Hess Oscar C J , van der Deure Tiem , Bolander Mille , Leal Dutra Caio A , Shik Jonathan Z
Published: October 2024

Fungi are abundant and ecologically important at a global scale, but little is known about whether their thermal adaptations are shaped by biochemical constraints (i.e., the hotter is better model) or evolutionary tradeoffs (i.e., the specialist-generalist model). We tested these hypotheses by generating thermal performance curves of fungal cultivars farmed by six species of Panamanian fungus-farming “attine” ants. These fungi represent evolutionary transitions in farming strategies, as four cultivars are farmed by ants below ground at stable temperatures near 25 °C and two cultivars are farmed above ground at variable temperatures. We generated thermal performance curves using a common garden experiment confining fungal isolates to different temperatures and then used a Bayesian hierarchical modelling approach to compare competing temperature sensitivity models. Some thermal performance traits differed consistently across farming strategies, with above-ground cultivars having: (1) higher tolerance to low temperatures (CTLmin) and (2) higher maximum growth rate at the optimal temperature (rmax). However, two core assumptions shared by the hotter is better model or specialist-generalist model were not supported as above-ground cultivars did not show systematic increases in either their optimal temperature (Topt) or thermal tolerance breadth. These results harness ant farming systems as long-term natural experiments to decouple the effects of environmental thermal variation and innate physiological temperature sensitivity on fungal thermal evolution. The results have clear implications for predicting climate warming-induced breaking points in animal-microbe mutualisms.
Eosinophil-airway epithelial cell crosstalk reveals the eosinophil-mediated DUOX1 upregulation in a murine allergic inflammation setting
Authors: Raggi Carla , Spadaro Francesca , Mattei Fabrizio , Gambardella Adriana Rosa , Noto Francesco , Andreone Sara , Signore Michele , Schiavoni Giovanna , Parolini Isabella , Afferni Claudia
Published: October 2024

Blood and airway eosinophilia represent markers for the endotype-driven treatment of allergic asthma. Little is known on mechanisms that link eosinophils and airway epithelial cells before and after these cells are infiltrated by eosinophils during allergic response. Given that innate immune mechanisms, mainly mediated by epithelial-derived cytokines (interleukin [IL]-33, IL-25, TSLP [thymic stromal lymphopoietin]), induce eosinophil-maturing/attractive substances, we thought to evaluate the crosstalk between eosinophils and airway epithelial cells in the context of IL-33–mediated allergic inflammation. DUOX1 was previously described in clinically relevant aspects of allergic inflammation in a HDM -induced allergic asthma mice model, and in patients with chronic sinusitis or allergic asthma. Thus, we evaluated the involvement of HDM and eosinophils in the regulation of DUOX1 in airway epithelial cells. To recapitulate the lung environment present at the allergen challenge time in acute asthma, we set up an in vitro model based on murine bone marrow–derived eosinophils differentiated with IL-5 and then activated with IL-33 (EOs33) and TC1 or C57 airway epithelial cells. We found that treatment of epithelial cells with HDM induced an eosinophil-attractive environment and increased DUOX1 expression. Importantly, we found that the coculture of airway epithelial cells with EOs33 or with conditioned medium from EOs33 enhanced the expression of DUOX1, which was further increased by combined stimulation (HDM plus EOs33). Our results suggest that lung recruited eosinophils once activated by IL-33 could be involved in a crosstalk loop with airway epithelial cells by DUOX1-mediated IL-33 secretion.
Characteristics of the IgM repertoires in the peripheral blood of early rheumatoid arthritis patients
Authors: Hong Binbin , Li Qiulan , Liu Qiaoling , Huang Rongfu , Wang Mei’er , Guo Ziyue , Huang Jiewei , Wang Jiaqi , Fan Chunmei , Ying Tianlei
Published: October 2024

Rheumatoid arthritis is a common autoimmune disease, but little is known about the characteristics of the B cell repertoires in the peripheral blood. In this study, the peripheral IgM repertoires of early rheumatoid arthritis (ERA) patients were analyzed by high-throughput sequencing and bioinformatics analyses. Clonal expansion was observed in IgM repertoires of ERA patients. Interestingly, a subset of the dominant clones in ERA repertoires showed self- and polyreactivity to several autoantigens. The clones were also identified in IgM repertoires of healthy adults but they were not expanded, suggesting that they may originate from the natural autoreactive B cell repertoire. Additionally, the ERA repertoires exhibited a greater extent of somatic hypermutations, particularly in the ERA dominant clones, resulting in an enrichment of amino acids important for antigen-antibody interaction. The in-depth analysis of B cell repertoires improved our knowledge of the IgM repertoires in ERA, offering potential insights into the disease's pathogenesis.
Variation in species-specific responses to habitat fragmentation and land cover structure in urban small mammal communities
Authors: Larson Rachel N , Sander Heather A
Published: October 2024

Urbanization is a key driver of habitat loss and fragmentation worldwide, yet many urban ecosystems contain vegetated habitat patches that support diverse wildlife communities. Managing urban systems to support robust wildlife communities requires us to understand the mechanisms that drive the response of species to the urban environment. Small mammals are key components of terrestrial ecosystems (e.g., seed predators, prey) and likely also carry out these roles in urban ecosystems; however, the effects of urbanization on small mammal communities are understudied. To identify how species-specific responses to urban environments shape community composition, we quantified both overall community and species-specific changes in small mammal abundance across an urbanization gradient in a Midwestern US metropolitan area. We combined small mammal trapping and land cover data to generate a hierarchical community abundance model. Species diversity increased with increasing proportional cover of human-modified land cover (i.e., impervious surfaces and turfgrass). This finding is driven by high species diversity on sites bordering streams in mowed parks and low diversity on sites with high tree canopy closure. Additionally, modeling results indicated that species responded differently to landscape attributes, leading to variation in small mammal community composition across the urbanization gradient: prairie-associated species tended to be more abundant in tall vegetation bordering mowed parks while habitat generalists tended to be more abundant on sites with greater canopy closure and shrub cover. Our results suggest that studies that focus on community-level responses (e.g., species richness) to urbanization may miss important species-specific responses. It may be particularly important to assess both species-specific and community-level responses in cities at ecotones (e.g., between forest and grassland) where species with different habitat requirements may replace one another in different types of green spaces, thereby changing community composition without affecting species diversity or richness. Our findings also indicate that vegetated urban patches, especially patches with tall vegetation cover and low canopy cover, are important habitat for prairie-associated small mammal communities, providing conservation options in heavily altered landscapes.
Narrative review of lifestyle interventions in breast cancer survivors: current evidence and future directions
Authors: Gabel Kelsey , Chakos Kaitlin , Oliveira Manoela Lima , Sanchez Perez Julienne , Cares Kate , Lima Natalia Salvatierra , Ganschow Pamela , Yanez Betina , Gadi Vijayakrishna , Tussing-Humphreys Lisa
Published: October 2024

Background

In 8 females, 1 will be diagnosed with breast cancer in their lifetime. Although medical advances have increased the likelihood of survival, up to 90% of females will gain weight during and after treatment increasing the risk of breast cancer recurrence and obesity-related comorbidities in survivorship. Behavioral lifestyle interventions focused on diet with or without physical activity can provide breast cancer survivors nonpharmacological options to decrease weight gain and cardiometabolic risk.

Method

A PubMed search was conducted to identify all behavioral lifestyle interventions focused on diet or diet combined with physical activity longer than 4 weeks of duration in breast cancer survivors that included body weight as an outcome. This review aims to summarize the effects on body weight, body composition, and cardiometabolic risk markers.

Results

The review shows there is high heterogeneity in type and duration of the intervention to affect weight and cardiometabolic risk in survivorship. Calorie restriction with and without physical activity appears to promote weight loss among breast cancer survivors. However, the effects on cardiometabolic factors are less clear.

Conclusions

Future studies should be powered for body weight and cardiometabolic effects. Researchers should also consider interventions that (1) are less complex, (2) recruit a more racially and ethnically diverse sample, (3) integrate resistance training, (4) implement the intervention in closer proximity to diagnosis, (5) target weight management in this population before it occurs, and (6) analyze body composition in addition to body weight measurements.
Hydrodynamic simulations of white dwarf–white dwarf mergers and the origin of R Coronae Borealis stars
Authors: Shiber Sagiv , De Marco Orsola , Motl Patrick M , Munson Bradley , Marcello Dominic C , Frank Juhan , Diehl Patrick , Clayton Geoffrey C , Skinner Bennett N , Kaiser Hartmut , Daiß Gregor , Pflüger Dirk , Staff Jan E
Published: October 2024

We study the properties of double white dwarf (DWD) mergers by performing hydrodynamic simulations using the new and improved adaptive mesh refinement code octo-tiger. We follow the orbital evolution of DWD systems of mass ratio $q=0.7$ for tens of orbits until and after the merger to investigate them as a possible origin for R Coronae Borealis (RCB) type stars. We reproduce previous results, finding that during the merger, the helium WD donor star is tidally disrupted within 20–80 min since the beginning of the simulation onto the accretor carbon–oxygen WD, creating a high temperature shell around the accretor. We investigate the possible helium burning in this shell and the merged object’s general structure. Specifically, we are interested in the amount of oxygen-16 dredged-up from the accretor to the hot shell and the amount of oxygen-18 produced. This is critical as the discovery of very low oxygen-16 to oxygen-18 ratios in RCB stars pointed out the merger scenario as a favourable explanation for their origin. A small amount of hydrogen in the donor may help keep the oxygen-16 to oxygen-18 ratios within observational bounds, even if moderate dredge-up from the accretor occurs. In addition, we perform a resolution study to reconcile the difference found in the amount of oxygen-16 dredge-up between smoothed-particle hydrodynamics and grid-based simulations.
Umbral flashes and their association with running penumbral waves: a study using MAST Ca ii 8542 Å narrow-band observations
Authors: Dubey Sandeep K , Mathew Shibu K , Bayanna A Raja
Published: October 2024

Umbral flashes (UFs) are one of the most dynamic phenomena observed in the sunspot umbra at the chromospheric heights. In this paper, we present spectroscopic observations of UFs in the Ca ii 8542 Å line recorded by a narrow-band imager working with the Multi-Application Solar Telescope (MAST). The deduced data are analysed to obtain various properties of the UFs occuring at different locations inside the umbral boundary. An intensity enhancement of up to 30% or more was observed at the location of UFs, with a periodicity $\approx$3 min. The line-of-sight (LOS) velocity of UFs was estimated using bisector application to the emission profile resulting from the removal of mean umbral and the mean quiet Sun (QS) line profiles. The emission profiles resulting from removing the mean umbral profile were observed to better represent the emission component of the UF line profile. Both up-flows and down-flows of the order $\approx$5 km s$^{-1}$ were associated with the UFs with an average up-flow of $\approx$1 km s$^{-1}$. Out of all UFs analysed, 31% were observed to be associated with down-flows in case of removal of the mean umbral profile from the UF line profile. We observed multiple radially propagating LOS velocity disturbances ($\approx$20–40 km s$^{-1}$) in the penumbra, which might be associated with the UFs, even though we could not establish a one-to-one correspondence. The horizontally propagating LOS velocity disturbances could produce the visual effect of running penumbral waves, which produce intensity fluctuations in intensity images when observed at the line-centre wavelength. The simultaneous photospheric HMI observations showed no distinct intensity or velocity signatures corresponding to the UFs observed in the chromospheric Ca ii 8542 Å line.
Genomic and Acoustic Biogeography of the Iconic Sulphur-crested Cockatoo Clarifies Species Limits and Patterns of Intraspecific Diversity
Authors: Sands Arthur F , Andersson Astrid A L , Reid Kerry , Hains Taylor , Joseph Leo , Drew Alex , Mason Ian J , Rheindt Frank E , Dingle Caroline , Merilä Juha
Published: October 2024

Many highly recognizable species lack genetic data important for conservation due to neglect over their hyperabundance. This likely applies to the Sulfur-crested Cockatoo (Cacatua galerita), one of the world's most iconic parrots. The species is native to Australia, New Guinea, and some surrounding Melanesian islands of the latter. Four subspecies are currently recognised based on morphology. Australian subspecies and populations are abundant, but several factors threaten those in New Guinea and Melanesia. Genetic data from natural populations are scarce—information that is vital to identifying evolutionarily significant units (ESUs) important for modern conservation planning. We used whole-genome resequencing to investigate patterns of differentiation, evolutionary affinities, and demographic history across C. galerita's distribution range to assess whether currently recognised subspecies represent ESUs. We complement this with an assessment of bioacoustic variation across the species' distribution landscape. Our results point to C. galerita sensu lato (s.l.) comprising two species. We restrict C. galerita sensu stricto (s.s.) to populations in Australia and the Trans-Fly ecodomain of southern New Guinea. The second species, recognised here as Cacatua triton, likely occurs over much of the rest of New Guinea. Restricting further discussion of intraspecific diversity in C. triton, we show that within C. galerita s.s. two ESUs exist, which align to Cacatua galerita galerita in eastern Australia and southern New Guinea and Cacatua galerita fitzroyi in northern and north-western Australia. We suggest that the evolution of these species and ESUs are linked to Middle and Late Pleistocene glacial cycles and their effects on sea level and preferential habitats. We argue that conservation assessments need updating, protection of preferential forest and woodland habitats are important and reintroductions require careful management to avoid possible negative hybridization effects of non-complementary lineages.
Nitrogen fertilizers activate siderophore production by the common scab causative agent Streptomyces scabiei
Authors: Stulanovic Nudzejma , Kerdel Yasmine , Belde Loïc , Rezende Lucas , Deflandre Benoit , Burguet Pierre , Denoel Romane , Tellatin Déborah , Rigolet Augustin , Hanikenne Marc , Quinton Loïc , Ongena Marc , Rigali Sébastien
Published: October 2024

Streptomyces scabiei is the causative agent of common scab on root and tuber crops. Life in the soil imposes intense competition between soil-dwelling microorganisms, and we evaluated here the antimicrobial properties of S. scabiei. Under laboratory culture conditions, increasing peptone levels correlated with increased growth inhibitory properties of S. scabiei. Comparative metabolomics showed that production of S. scabiei siderophores (desferrioxamines, pyochelin, scabichelin, and turgichelin) increased with the quantity of peptone, thereby suggesting that they participate in growth inhibition. Mass spectrometry imaging further confirmed that the zones of secreted siderophores and growth inhibition coincided. Moreover, either the repression of siderophore production or the neutralization of their iron-chelating activity led to increased microbial growth. Replacement of peptone by natural nitrogen sources regularly used as fertilizers such as ammonium nitrate, ammonium sulfate, sodium nitrate, and urea also triggered siderophore production in S. scabiei. The observed effect is not mediated by alkalinization of the medium as increasing the pH without providing additional nitrogen sources did not induce siderophore production. The nitrogen-induced siderophore production also inhibited the growth of important plant pathogens. Overall, our work suggests that not only the iron availability but also the nitrogen fertilizer sources could significantly impact the competition for iron between crop-colonizing microorganisms.
RNase W, a conserved ribonuclease family with a novel active site
Authors: Vayssières Marlène , Jüttner Michael , Haas Karina , Ancelin Aurélie , Marchfelder Anita , Leulliot Nicolas , Ferreira-Cerca Sébastien , Blaud Magali
Published: October 2024

Ribosome biogenesis is a complex process requiring multiple precursor ribosomal RNA (rRNA) cleavage steps. In archaea, the full set of ribonucleases (RNases) involved in rRNA processing remains to be discovered. A previous study suggested that FAU-1, a conserved protein containing an RNase G/E-like protein domain fused to a domain of unknown function (DUF402), acts as an RNase in archaea. However, the molecular basis of this activity remained so far elusive. Here, we report two X-ray crystallographic structures of RNase G/E-like–DUF402 hybrid proteins from Pyrococcus furiosus and Sulfolobus acidocaldarius, at 2.1 and 2.0 Å, respectively. The structures highlight a structural homology with the 5′ RNA recognition domain of Escherichia coli RNase E but no homology with other known catalytic nuclease domains. Surprisingly, we demonstrate that the C-terminal domain of this hybrid protein, annotated as a putative diphosphatase domain, harbors the RNase activity. Our functional analysis also supports a model by which the RNase G/E-like domain acts as a regulatory subunit of the RNase activity. Finally, in vivo experiments in Haloferax volcanii suggest that this RNase participates in the maturation of pre-16S rRNA. Together, our study defines a new RNase family, which we termed the RNase W family, as the first archaea-specific contributor to archaeal ribosome biogenesis.
Coronavirus S protein alters dsRNA accumulation and stress granule formation through regulation of ADAR1-p150 expression
Authors: Fan Baochao , Li Yupeng , Wang Yi , Yang Shanshan , Peng Qi , Qian Jiali , Wang Chuanhong , Zhang Xue , Xu Hong , Liu Shiyu , He Wenlong , Zhang Gege , Zhu Xuejiao , Li Yunchuan , Zhao Yongxiang , Hu Mi , Wang Wei , Zhou Jinzhu , Guo Rongli , He Kongwang , Li Bin
Published: October 2024

The precise role of the highly variable coronavirus S protein in modulating innate immune responses remains unclear. In this study, we demonstrated that the mutant strain of swine coronavirus porcine enteric diarrhea virus induced significantly lower levels of double-stranded RNA (dsRNA) accumulation, inhibited protein kinase R (PKR) activation and suppressed stress granule (SG) formation compared with the classical strain. The 29th amino acid at N-terminus of S was identified as the key functional site for regulation of SG formation, and found that mutant S inhibited PKR phosphorylation and SG formation by upregulating adenosine deaminase acting on RNA 1 (ADAR1)-p150. Notably, the Zα domain of ADAR1-p150 was essential for inhibiting SG formation. Upregulation of ADAR1-p150 also reduced accumulation of dsRNA depending on its RNA editing function. Virus rescue confirmed that the mutant carrying a substitution at amino acid 29 failed to induce ADAR1-p150, leading to dsRNA accumulation, PKR activation and SG formation. Interestingly, the latest severe acute respiratory syndrome coronavirus-2 strains exhibit a novel 25PPA27 deletion at N-terminus of S that was also shown to lead to altered ADAR1-p150 expression and SG inhibition. The transcription factor TCF7L2 was identified as a player in S-mediated transcriptional enhancement of ADAR1-p150. This study is the first to clarify the crucial role of N-terminus of S in immune regulation of coronaviruses.
Intronic RNA secondary structural information captured for the human MYC pre-mRNA
Authors: Eich Taylor O , O’Leary Collin A , Moss Walter N
Published: October 2024

To address the lack of intronic reads in secondary structure probing data for the human MYC pre-mRNA, we developed a method that combines spliceosomal inhibition with RNA probing and sequencing. Here, the SIRP-seq method was applied to study the secondary structure of human MYC RNAs by chemically probing HeLa cells with dimethyl sulfate in the presence of the small molecule spliceosome inhibitor pladienolide B. Pladienolide B binds to the SF3B complex of the spliceosome to inhibit intron removal during splicing, resulting in retained intronic sequences. This method was used to increase the read coverage over intronic regions of MYC. The purpose for increasing coverage across introns was to generate complete reactivity profiles for intronic sequences via the DMS-MaPseq approach. Notably, depth was sufficient for analysis by the program DRACO, which was able to deduce distinct reactivity profiles and predict multiple secondary structural conformations as well as their suggested stoichiometric abundances. The results presented here provide a new method for intronic RNA secondary structural analyses, as well as specific structural insights relevant to MYC RNA splicing regulation and therapeutic targeting.
Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota
Authors: Liu Lan , Lian Zheng-Han , Lv Ai-Ping , Salam Nimaichand , Zhang Jian-Chao , Li Meng-Meng , Sun Wei-Min , Tan Sha , Luo Zhen-Hao , Gao Lei , Yuan Yang , Ming Yu-Zhen , OuYang Yu-Ting , Li Yu-Xian , Liu Ze-Tao , Hu Chao-Jian , Chen Ying , Hua Zheng-Shuang , Shu Wen-Sheng , Hedlund Brian P , Li Wen-Jun , Jiao Jian-Yu
Published: October 2024

Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood–Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.
Unraveling the Effects of Economic Growth and Unemployment on Tobacco Use: A Panel Data Approach
Authors: Savaş Yunus , Erat Veysel , Alma Savaş Dilek
Published: October 2024

Introduction

The economic situation is recognized as a significant factor influencing tobacco consumption. Accordingly, this research aims to investigate the relationship between economic growth, unemployment, and tobacco use.

Methods

This investigation employs data from 1985 to 2019 to elucidate the relationship between economic growth, unemployment, and tobacco consumption in a select group of Organization for Economic Co-operation and Development countries. Employing Pedroni and Johansen–Fisher panel co-integration tests, we assess the co-integrating relationships. Furthermore, FMOLS and DOLS techniques are applied, complemented by the Dumitrescu–Hurlin panel causality test.

Results

FMOLS and DOLS results suggest that a 1% increase in gross domestic product (GDP) leads to a 6.46% and 7.29% rise in tobacco consumption, respectively, while GDP squared results in a 0.39% and 0.43% decrease. However, both tests failed to establish a significant relationship between tobacco consumption and unemployment. Co-integration was confirmed by Johansen–Fisher and Pedroni tests. Dumitrescu–Hurlin causality tests revealed the direction of Granger causality from economic growth to tobacco consumption, but not with unemployment.

Conclusion

Tobacco consumption declined across all countries studied. Economic growth shows a positive association, while GDP squared has a negative association, indicating an inverted U-shaped relationship. No significant relationship was found with unemployment in the employed tests.

Implications

In addition to the measures implemented by countries to reduce tobacco consumption, economic factors also exert a significant relation with smoking behavior. The available results suggest that economic growth is initially associated with an increase in tobacco consumption but the reduction in later stages indicating a long-term inverse relationship between economic growth and tobacco use.
Comparison of Waning Antibody Responses After Natural Monkeypox Virus Infection and Mpox Vaccination Beyond 6 Months in South Korea
Authors: Lim So Yun , Kim Hyang Su , Yim Hong Soon , Kim Hyesu , Han In Ae , Yoon Doran , Kim Min-Kyung , Kim Yeonjae , Um Jihye , Kim Gayeon , Chin BumSik , Park Jun-Sun , Bang Jihwan
Published: October 2024

Natural Monkeypox virus infection induced significantly higher neutralizing antibody titers than Jynneos vaccination, with similar antibody decay rates beyond 6 months. Jynneos recipients with prior smallpox vaccination showed antibody levels comparable to mpox convalescents.
Quantifying and Adjusting for Confounding From Health-Seeking Behavior and Health Care Access in Observational Research
Authors: Graham Sophie , Walker Jemma L , Andrews Nick , Hulme William J , Nitsch Dorothea , Parker Edward P K , McDonald Helen I
Published: October 2024

Background

Health-seeking behavior and health care access (HSB/HCA) are recognized confounders in many observational studies but are not directly measurable in electronic health records. We used proxy markers of HSB/HCA to quantify and adjust for confounding in observational studies of influenza and COVID-19 vaccine effectiveness (VE).

Methods

This cohort study used primary care data prelinked to secondary care and death data in England. We included individuals aged ≥66 years on 1 September 2019 and assessed influenza VE in the 2019–2020 season and early COVID-19 VE (December 2020–March 2021). VE was estimated with sequential adjustment for demographics, comorbidities, and 14 markers of HSB/HCA. Influenza vaccination in the 2019–2020 season was also considered a negative control exposure against COVID-19 before COVID-19 vaccine rollout.

Results

We included 1 991 284, 1 796 667, and 1 946 943 individuals in the influenza, COVID-19, and negative control exposure populations, respectively. Markers of HSB/HCA were positively correlated with influenza and COVID-19 vaccine uptake. For influenza, adjusting for HSB/HCA markers in addition to demographics and comorbidities increased VE against influenza-like illness from −1.5% (95% CI, −3.2% to .1%) to 7.1% (95% CI, 5.4%–8.7%) with a less apparent trend for more severe outcomes. For COVID-19, adjusting for HSB/HCA markers did not change VE estimates against infection or severe disease (eg, 2 doses of BNT162b2 against infection: 82.8% [95% CI, 78.4%–86.3%] to 83.1% [95% CI, 78.7%–86.5%]). Adjusting for HSB/HCA markers removed bias in the negative control exposure analysis (−7.5% [95% CI, −10.6% to −4.5%] vs −2.1% [95% CI, −6.0% to 1.7%] before vs after adjusting for HSB/HCA markers).

Conclusions

Markers of HSB/HCA can be used to quantify and account for confounding in observational vaccine studies.