bluuebunny/crossref_metadata_2025 huggingface dataset:
ghosts, Mesopotamia
Authors: Heinrich Adrian Cornelius
Published: November 2024

The Old Babylonian Atrahasīs epic details the creation of man from clay mixed with the flesh and blood of an immortal god. Accordingly, in ancient Mesopotamia, humans were thought to have a part that survived death. This surviving part was called “ghost” (eṭemmu in Akkadian/gedim in Sumerian). After a proper burial, the ghosts of the dead dwelled in the netherworld, a distant part of the cosmos governed by the goddess Ereshkigal and her spouse Nergal. Since ghosts not only preserved part of their former human identity but also hunger, thirst, and the need for attention, their peaceful rest depended on the care offered by their living kin in the form of the offerings and commemorative rites that constituted the core of Mesopotamian family religion. If these funerary rituals were neglected or a corpse was not buried properly, ghosts turned into restlessly roaming or evil ghosts that plagued the living, akin to demons, and caused all kinds of distress.

With regard to the modern study of ideas and practices related to ghosts in Mesopotamia, the corpus of cuneiform texts dealing with rituals against ghosts and the phenomenology of ghostly apparitions from 1st-millennium Babylonia and Assyria stands out as a particularly rich source of information. Other essential materials include Sumerian and Akkadian literary texts that describe images of the netherworld, burial sites, and related funerary objects that offer archaeological evidence for cultural concepts and related practices about death and the afterlife. However, due to the vast chronological, geographical, and typological scope of the sources, the modern study of the Mesopotamian ghost still faces fundamental research challenges, such as comprehending the distinction between the ghosts of the dead, on the one hand, and different other ghost-like beings, such as demons or the zaqīqu-phantom, a phenomenon comparable to the concept of a “dream soul” in other cultures, on the other.
Modern Urban Multiethnolects of Germanic Languages
Authors: Quist Pia
Published: November 2024

Modern Urban Multiethnolects of Germanic languages refer to diverse ways of speaking Germanic languages in multilingual environments, typically found in major cities like Berlin, Utrecht, and Oslo. While European cities have historically been multilingual, post–World War II immigration has created new linguistic contact zones, providing the context for the emergence of novel speech practices, particularly among young people. Researchers have investigated these practices and identified several linguistically characteristic features. Notably, some of these features exhibit parallels across Germanic-speaking countries. For instance, research has documented systematic variation in the syntactic verb second constraint (V2), variation in the use of grammatical gender marking, the use of loanwords from languages such as Turkish and Arabic, and not least nonstandard ways of pronouncing the local languages including both supra-segmental (such as tone, stress pattern, and intonation) and segmental phonological features. While some studies on multiethnolects have focused on documenting such grammatical and phonetic features, other studies have explored socio-pragmatic functions and social practices associated with the emergence of multiethnolects. Different scholarly approaches intersect, with some studies combining perspectives in both structural and social practices. Other studies again have examined the extent to which the new multiethnolectal ways of speaking correlate with local dialect variation. In some urban areas, speakers integrate features from both multiethnolects and local dialects. In other contexts, multiethnolects remain distinct, resisting assimilation into existing dialect variation. Altogether, the broad range of studies, and their different approaches and foci, not only underscores the complexity of multiethnolectal variation, but also the fact that multiethnolects are by nature highly dynamic and fluid.
The Health–Disaster Risk Interface 1970–2020: Evolution, (Dis)Articulation, and Realignment
Authors: Holloway Ailsa
Published: November 2024

While the health sector’s operational role in emergencies and disasters is well- acknowledged and respected, health has also contributed substantially to the historical, conceptual, and methodological maturation of the disaster risk domain, especially since the 1970s. From 1970 to 2020, this evolution of the health–disaster risk knowledge interface can be understood through four phases. The first, from the late 1970s until 1989, was characterized by a surge in emergency health responses across a succession of disasters triggered by hydrometeorological and geophysical processes as well as humanitarian emergencies. The 1970–1989 period also saw the establishment of new health-specific emergency architectures and knowledge domains. The second phase, from 1990 until the early 2000s, was substantially influenced by global mechanisms, including the United Nations designation of the 1990s as the International Decade for Natural Disaster Reduction. The third phase, emerging in the early 2000s, profiled the changing global configuration of risk and disaster, with disaster impacts, including health effects, becoming more pronounced in high-income countries. The onset of the fourth phase was signaled by the 2015 global landmark agreements: the Sendai Framework for Disaster Risk Reduction, the Paris Agreement on climate change, and the 2030 Agenda for Sustainable Development.

The Sendai Framework for Disaster Risk Reduction is recognized for exceeding the scope of its predecessor agreements by foregrounding health as an integral concern of disaster risk reduction. Health’s enhanced visibility through the Sendai Framework was paralleled by other processes that reinforced understanding of the health–disaster risk interface. These included initiatives on One Health and Planetary Health, as well as growing awareness of the health implications of climate change.

This synergistic potential of the health–disaster risk knowledge interface draws from the strong conceptual alignment across both domains. This reflects explicit coherence between the core concept of “health determinants” (the social, physical, and other forces) that shape health outcomes and the disaster risk-related concepts of hazard, vulnerability, exposure, and capacity, which similarly configure disaster risk.

Since 2015, recognition of the significance of this alignment has accelerated efforts to promote more resilient health systems as well as cross-field initiatives such as Health Emergency and Disaster Risk Management. With hazard processes, especially those linked to climate extremes, exacting increased demands on health care systems, there is urgency for even greater innovation at the health–disaster risk knowledge interface.
Institutional Racism and Effects on Health and Well-Being
Authors: Copeland Valire Carr , Wexler Sandra , Braxter Betty
Published: November 2024

Racial inequality negatively influences the lives of people of color in the United States. Although race refers to differential concentrations of specific genes, the impacts are confined to physical characteristics such as skin color, hair type, and eye color. Rather than designating meaningful biological categories, race is a social construct. Yet, where there are inevitable intersections with institutional structures and interpersonal health relationships, race and racism produce inequities.

Racism occurs within and permeates the overarching political, social, cultural, and economic systems of American society. It can take several forms: structural, institutional, interpersonal, and internalized. Institutional racism in the healthcare system yields adverse effects on the physical and mental health and well-being of racialized individuals and communities. These inequities are well documented.

Recommendations are offered for creating a fairer and more just healthcare system in America. Equality and equity in the country’s healthcare system will be achieved only if racism is challenged in all its forms.
A review of potential biological controls for Ailanthus altissima
Authors: Miles Harrison H , Salom Scott , Shively Timothy J , Bielski Jason T , McAvoy Thomas J , Fearer Carrie J
Published: November 2024

Ailanthus altissima (Mill.) Swingle (Sapindales: Simaroubaceae) (tree-of-heaven) is an invasive tree species first introduced to the United States in 1784. With high rates of sexual reproduction, rapid growth, and prolific vegetative sprouting, A. altissima is an aggressive competitor that reduces native plant diversity and is difficult to manage beyond small-scale infestations. In the United States, the issues associated with Ailanthus management were compounded by the 2014 arrival of Lycorma delicatula (spotted lanternfly). Lycorma delicatula coevolved with A. altissima, its primary host, in eastern Asia. Suppression of A. altissima is recommended as an important strategy to slow the spread of L. delicatula. Due to the inadequacy of traditional control methods to manage A. altissima, biological controls are desired. Several potential biological control agents have been proposed for A. altissima. This review discusses current research on several promising candidates, specifically a native fungus, Verticillium nonalfalfae Inderb. et al. (Hypocreales: Plectosphaerellaceae); a trunk-boring beetle, Eucryptorrhynchus brandti (Harold) (Coleoptera: Curculionidae: Cryptorrhynchinae); and an eriophyid mite, Aculops ailanthi (Lin-Fuping, Jin-Changle & Kuang-Haiya) (Arachnida: Eriphyidae). A list of other possible biological control agents is also provided. We discuss unanswered questions for each species, the limits of biological controls in this system, and call for further research on integrated pest management practices for managing A. altissima.
SIngle cell level Genotyping Using scRna Data (SIGURD)
Authors: Grasshoff Martin , Kalmer Milena , Chatain Nicolas , Kricheldorf Kim , Maurer Angela , Weiskirchen Ralf , Koschmieder Steffen , Costa Ivan G
Published: November 2024

Motivation: By accounting for variants within measured transcripts, it is possible to evaluate the status of somatic variants using single-cell RNA-sequencing (scRNA-seq) and to characterize their clonality. However, the sparsity (very few reads per transcript) or bias in protocols (favoring 3’ ends of the transcripts) makes the chance of capturing somatic variants very unlikely. This can be overcome by targeted sequencing or the use of mitochondrial variants as natural barcodes for clone identification. Currently, available computational tools focus on genotyping, but do not provide functionality for combined analysis of somatic and mitochondrial variants and functional analysis such as characterization of gene expression changes in detected clones. Results: Here, we propose SIGURD (SIngle cell level Genotyping Using scRna Data) (SIGURD), which is an R-based pipeline for the clonal analysis of scRNA-seq data. This allows the quantification of clones by leveraging both somatic and mitochondrial variants. SIGURD also allows for functional analysis after clonal detection: association of clones with cell populations, detection of differentially expressed genes across clones, and association of somatic and mitochondrial variants. Here, we demonstrate the power of SIGURD by analyzing single-cell data of colony-forming cells derived from patients with myeloproliferative neoplasms.
The ISCB competency framework v. 3: a revised and extended standard for bioinformatics education and training
Authors: Brooksbank Cath , Brazas Michelle D , Mulder Nicola , Schwartz Russell , Ras Verena , Morgan Sarah L , Lloret Llinares Marta , Carvajal López Patricia , Larcombe Lee , Ghouila Amel , Hancocks Tom , Satagopam Venkata , De Las Rivas Javier , Mazandu Gaston , Gaeta Bruno
Published: November 2024

Motivation

Developing competency in the broad area of bioinformatics is challenging globally, owing to the breadth of the field and the diversity of its audiences for education and training. Course design can be facilitated by the use of a competency framework—a set of competency requirements that define the knowledge, skills and attitudes needed by individuals in (or aspiring to be in) a particular profession or role. These competency requirements can help to define curricula as they can inform both the content and level to which competency needs to be developed. The International Society for Computational Biology (ISCB) developed a list of bioinformatics competencies in 2014, and these have undergone several rounds of improvement. In consultation with a broad bioinformatics training community, these have now been further refined and extended to include knowledge skills and attitudes, and mappings to previous and other existing competency frameworks.

Results

Here, we present version 3 of the ISCB competency framework. We describe how it was developed and how to access it, as well as providing some examples of how it has been used.

Availability and implementation

The framework is openly accessible at https://competency.ebi.ac.uk/framework/iscb/3.0/competencies.
Dynamic modelling of signalling pathways when ordinary differential equations are not feasible
Authors: Rachel Timo , Brombacher Eva , Wöhrle Svenja , Groß Olaf , Kreutz Clemens
Published: November 2024

Motivation

Mathematical modelling plays a crucial role in understanding inter- and intracellular signalling processes. Currently, ordinary differential equations (ODEs) are the predominant approach in systems biology for modelling such pathways. While ODE models offer mechanistic interpretability, they also suffer from limitations, including the need to consider all relevant compounds, resulting in large models difficult to handle numerically and requiring extensive data.

Results

In previous work, we introduced the retarded transient function (RTF) as an alternative method for modelling temporal responses of signalling pathways. Here, we extend the RTF approach to integrate concentration or dose-dependencies into the modelling of dynamics. With this advancement, RTF modelling now fully encompasses the application range of ODE models, which comprises predictions in both time and concentration domains. Moreover, characterizing dose-dependencies provides an intuitive way to investigate and characterize signalling differences between biological conditions or cell types based on their response to stimulating inputs. To demonstrate the applicability of our extended approach, we employ data from time- and dose-dependent inflammasome activation in bone marrow-derived macrophages treated with nigericin sodium salt. Our results show the effectiveness of the extended RTF approach as a generic framework for modelling dose-dependent kinetics in cellular signalling. The approach results in intuitively interpretable parameters that describe signal dynamics and enables predictive modelling of time- and dose-dependencies even if only individual cellular components are quantified.

Availability and implementation

The presented approach is available within the MATLAB-based Data2Dynamics modelling toolbox at https://github.com/Data2Dynamics and https://zenodo.org/records/14008247 and as R code at https://github.com/kreutz-lab/RTF.
Damsel: analysis and visualisation of DamID sequencing in R
Authors: Page Caitlin G , Lonsdale Andrew , Mitchell Katrina A , Schröder Jan , Harvey Kieran F , Oshlack Alicia
Published: November 2024

DamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor package to provide an end to end analysis for DamID sequencing data within R. Damsel performs quantification and testing of significant binding sites along with exploratory and visual analysis. Damsel produces results consistent with previous analysis approaches.

Availability and implementation

The R package Damsel is available for install through the Bioconductor project https://bioconductor.org/packages/release/bioc/html/Damsel.html and the code is available on GitHub https://github.com/Oshlack/Damsel/.
Democracy, Egalitarianism and the Homicide Rate: An Empirical Test of a Variety of Democracies, 1990–2019
Authors: de Soysa Indra
Published: November 2024

Democracy and the level of economic development correlate tightly. While some argue that egalitarian conditions inherent in democracies reduce homicide, others suggest that it is economic development that matters. This study evaluates competing theory and tests the democracy—homicide link using homicide data defined as death due to interpersonal violence and novel data on a variety of democracies. The results show that democracies associate positively with homicide, and egalitarian democracy shows the strongest effect. The level of economic development is negative on homicide and substantively large. The basic results are robust to alternative data, estimating method, and to omitted variables bias.
Rituximab as a first-line therapy in children with new-onset idiopathic nephrotic syndrome
Authors: Zhang Xiaojing , Jin Yanyan , Liu Fei , Li Qiuyu , Xie Yi , Huang Guoping , chen Junyi , He Xue , He Siyi , Fu Haidong , Wang Jingjing , Shen Huijun , Mao Jianhua
Published: November 2024

Background

Idiopathic nephrotic syndrome (INS) in children, commonly treated with steroids, poses challenges due to associated side effects. Rituximab, known for its efficacy in reducing relapse frequency in difficult-to-treat cases, emerges a potential first-line therapy for pediatric new-onset INS.

Method

This is a single-center, retrospective, observational study to evaluate the efficacy and safety of rituximab as a first-line therapy for pediatric INS. The complete treatment strategy was weekly injections at a dose of 375 mg/m2 for four doses. Children with new-onset INS who received rituximab as a first-line monotherapy from 1 January 2022 to 31 December 2023 were included and followed until 31 May 2024.

Results

Seventeen patients (median age at diagnosis 4.8 years) were included. Twelve patients achieved complete remission within a median time of 19 days. Over a follow-up period ranging from 41 to 112 weeks, 11 patients maintained remission even after B-cell reconstitution, with one patient experiencing a relapse at 85 weeks. Three patients, who presented with hematuria, hypocomplementemia or renal injury at initial diagnosis, exhibited resistance to rituximab. No severe adverse events were noted.

Conclusion

Rituximab may be an effective and safe option as a first-line therapy for inducing and maintaining remission in newly diagnosed INS.
MUC1-associated autosomal dominant tubulointerstitial kidney disease: prevalence in kidney failure of undetermined aetiology and clinical insights from Danish families
Authors: Granhøj Jeff , Lildballe Dorte L , Pedersen Katja V , Tougaard Birgitte G , Sokol Martin , Aagaard Mads M , Petersen Annabeth H , Kristensen Tilde , Djursby Malene , Birn Henrik , Rasmussen Maria
Published: November 2024

Background

Frameshift variants in the variable number tandem repeat region of mucin-1 (MUC1) cause autosomal dominant tubulointerstitial kidney disease (ADTKD-MUC1) but are challenging to detect. We investigated the prevalence in patients with kidney failure of undetermined aetiology and compared Danish families with ADTKD-MUC1.

Methods

We recruited patients with suspected kidney failure of undetermined aetiology at ≤50 years and excluded those with a clear-cut clinical or histopathological kidney diagnoses or established genetic kidney diseases identified thorough medical record review. MUC1 genotyping was performed by SNaPshot analysis, detecting the most common pathogenic cytosine duplication, followed by bioinformatics pipeline VNtyper analysis of short-read sequencing data.

Results

Of 172 recruited patients, 123 underwent SNaPshot analyses, which were abnormal in 5/123 patients (4%). Next, VNtyper genotyping was performed in all patients, including the five with abnormal SNaPshot analysis. VNtyper re-identified the common cytosine duplication in all five patients and revealed novel frameshift variants in two additional patients, while the analyses were normal in the remaining 116 patients. All patients carrying frameshift variants in MUC1 fulfilled ADTKD criteria and had a family history of kidney failure. A considerable inter- and intrafamilial variability of chronic kidney disease stage relative to age was observed in families with ADTKD-MUC1.

Conclusions

ADTKD-MUC1 was identified in 7/123 patients (6%) in a selected cohort of kidney failure of undetermined aetiology ≤50 years, and VNtyper effectively identified all pathogenic MUC1 variants.
Variation in reproductive photosynthetic compensation of distinct germplasm varieties of a native rangeland grass, Pseudoroegneria spicata, following floral defoliation
Authors: Quigley Kathleen M , O’Connor Rory C , Monaco Thomas A , Hamerlynck Erik P
Published: November 2024

Understanding plant ecophysiological functioning is critical in formulating effective ecologically based strategies to conserve and enhance resiliency and resistance in sagebrush steppe, as well as improving their restoration following degradation by interactive effects of climate change, wildland fire and invasive annual grasses. Recent research has shown increased reproductive photosynthesis following floral defoliation can be important to reproductive potential, yet how this is expressed in plant material selected for different functional attributes is unknown. To address this, we measured photosynthetic gas exchange in clipped and unclipped basal florets and flag leaves of two germplasms of the native perennial bunchgrass, bluebunch wheatgrass, var. Anatone and var. Columbia, selected for higher reproductive culm production. Clipping induced a stronger direct compensatory reproductive photosynthetic response in basal florets of Anatone compared to Columbia germplasm individuals, with no indirect compensatory response apparent in unaffected distal florets of either germplasm. Flag-leaf photosynthesis did not differ between the germplasm lines, but Columbia flag leaves did show evidence of increased photosynthesis on culms with clipped basal florets. These findings suggest selection for increased flowering culms may alter reproductive herbivory tolerance, a feature important in the convergence of herbivory and drought tolerance traits. Such information could help in planning effective seed mixes to enhance population stability across highly variable sagebrush steppe ecosystems, as well as directing future plant material selection to improve restoration success in these economically important rangelands.
Device-related adverse events and flow capacity of percutaneous ventricular assist devices
Authors: Ikeda Yuki , Ishii Shunsuke , Nakahara Shohei , Iikura Saeko , Fujita Teppei , Iida Yuichiro , Nabeta Takeru , Sato Nobuhiro , Ako Junya
Published: November 2024

Aims

Complication management is crucial in patients receiving mechanical circulatory devices. However, there are limited data on the association between the risks of complications and device type in patients with percutaneous ventricular assist devices (PVAD).

Methods and results

The Japanese registry for PVAD (J-PVAD) is a nationwide ongoing registry that enrols consecutive patients with cardiogenic shock treated with PVAD. We analysed 5717 patients in the J-PVAD from 1 February 2020 to 31 December 2022, to compare the incident risks of device-related problems and all-cause mortality within 30 days after PVAD introduction based on flow capacities of first-line PVAD (low: Impella 2.5/CP, n = 5375; high: Impella 5.0/5.5, n = 342). The overall incidence of major device-related problems, including haemolysis, major bleeding, kidney injury, sepsis, and pump stop, was 13%, 21%, 7%, 3%, and 1%, respectively. The all-cause mortality rate was 34%. The incident risks of haemolysis [hazard ratio (HR) 0.38, 95% confidence interval (CI) 0.24–0.58], kidney injury (HR 0.32, 95% CI 0.18–0.57), and pump stop (HR 0.38, 95% CI 0.16–0.91) were lower in patients with high-flow PVAD compared with those with low-flow PVAD. The risks of major bleeding or sepsis did not differ significantly between groups. The risk of all-cause mortality was lower in patients with high-flow PVAD compared with those with low-flow PVAD (HR 0.79, 95% CI 0.65–0.96).

Conclusion

Compared with those with low-flow PVAD, patients with high-flow PVAD had lower incident risks of device-related problems, including haemolysis, kidney injury, and pump stop, as well as lower risk of all-cause mortality.
Adaptation During the Shift from Entomopathogen to Endosymbiont Is Accompanied by Gene Loss and Intensified Selection
Authors: Ward Chris M , Onetto Cristobal A , Borneman Anthony R
Published: November 2024

Fungi have been found to be associated with many insect species, with some species transitioning to reside within insects as symbionts. However, the evolutionary pressures and genomic consequences associated with this transition are not well understood. Pathogenic fungi of the genus Ophiocordyceps have undergone multiple, independent transitions from pathogen to endosymbiont lifestyles, where they reside within the fatty tissues of infected soft-scale insects transgenerationally without killing their hosts. To gain an understanding of the genomic adaptations underlying this life history shift, long-read sequencing was utilized to assemble the genomes of both the soft-scale insect Parthenolecanium corni and its Ophiocordyceps endosymbiont from a single insect. Assembly and metagenomic-based binning produced a highly contiguous genome for Pa. corni and a chromosome-level assembly for the Ophiocordyceps endosymbiont. The endosymbiont genome was characterized by 524 gene loss events compared to free-living pathogenic Ophiocordyceps relatives, with predicted roles in hyphal growth, cell wall integrity, metabolism, gene regulation, and toxin production. Contrasting patterns of selection were observed between the nuclear and mitochondrial genomes specific to the endosymbiont lineage. Intensified selection was most frequently observed across orthologs in the nuclear genome, whereas selection on most mitochondrial genes was found to be relaxed. Scans for positive selection were enriched within the fatty acid metabolism pathway with endosymbiont specific selection within three adjacent enzymes catalyzing the conversion of acetoacetate to acetyl-coenzyme A, suggesting that the endosymbiont lineage is under selective pressure to effectively exploit the lipid rich environment of the insect fat bodies in which it is found.
Bayesian hierarchical hypothesis testing in large-scale genome-wide association analysis
Authors: Samaddar Anirban , Maiti Tapabrata , de los Campos Gustavo
Published: November 2024

Variable selection and large-scale hypothesis testing are techniques commonly used to analyze high-dimensional genomic data. Despite recent advances in theory and methodology, variable selection and inference with highly collinear features remain challenging. For instance, collinearity poses a great challenge in genome-wide association studies involving millions of variants, many of which may be in high linkage disequilibrium. In such settings, collinearity can significantly reduce the power of variable selection methods to identify individual variants associated with an outcome. To address such challenges, we developed a Bayesian hierarchical hypothesis testing (BHHT)—a novel multiresolution testing procedure that offers high power with adequate error control and fine-mapping resolution. We demonstrate through simulations that the proposed methodology has a power-FDR performance that is competitive with (and in many scenarios better than) state-of-the-art methods. Finally, we demonstrate the feasibility of using BHHT with large sample size (n∼ 300,000) and ultra dimensional genotypes (∼ 15 million single-nucleotide polymorphisms or SNPs) by applying it to eight complex traits using data from the UK-Biobank. Our results show that the proposed methodology leads to many more discoveries than those obtained using traditional SNP-centered inference procedures. The article is accompanied by open-source software that implements the methods described in this study using algorithms that scale to biobank-size ultra-high-dimensional data.
A tale of two serines: the effects of histone H2A mutations S122A and S129A on chromosome nondisjunction in Saccharomyces cerevisiae
Authors: Kozmin Stanislav G , Dominska Margaret , Kokoska Robert J , Petes Thomas D
Published: November 2024

Near the C-terminus of histone H2A in the yeast Saccharomyces cerevisiae, there are 2 serines (S122 and S129) that are targets of phosphorylation. The phosphorylation of serine 129 in response to DNA damage is dependent on the Tel1 and Mec1 kinases. In Schizosaccharomyces pombe and S. cerevisiae, the phosphorylation of serine 122 is dependent on the Bub1 kinase, and S. pombe strains with an alanine mutation of this serine have elevated levels of lagging chromosomes in mitosis. Strains that lack both Tel1 and Mec1 in S. cerevisiae have very elevated rates of nondisjunction. To clarify the functional importance of phosphorylation of serines 122 and 129 in H2A, we measured chromosome loss rates in single-mutant strains and double-mutant combinations. We also examined the interaction of mutations of BUB1, TEL1, and MEC1 in combination with mutations of serines 122 and 129 in H2A. We conclude that the phosphorylation state of S129 has no effect on chromosome disjunction whereas mutations that inactivate Bub1 or a S122A mutation in the histone H2A greatly elevate the rate of chromosome nondisjunction. Based on this analysis, we suggest that Bub1 exerts its primary effect on chromosome disjunction by phosphorylating S122 of histone H2A. However, Tel1, Mec1, and Bub1 are also functionally redundant in a second pathway affecting chromosome disjunction that is at least partially independent of phosphorylation of S122 of H2A.
Where Do We Draw the Line? Perceptions of Abuse of Older Adults and Their Association With Ageism
Authors: Storey Jennifer E , O’Brien Rhianna C , Fraga Dominguez Silvia
Published: November 2024

Objectives

Violence against older adults is a prevalent global harm, and there is evidence that perceptions of violence toward older adults may affect reporting and intervention. The present study examines the perception of violence against older adults in contrast to violence against other age groups and investigates the role of ageism in those perceptions.

Methods

A total of 290 participants were surveyed and asked to indicate whether they perceived 15 abusive behaviors reflecting physical, psychological, sexual, and financial abuse and neglect to be abuse toward either an older adult (age 60+), adult, or child. Ageism was measured using the Ambivalent Ageism scale.

Results

On average, 25% of participants did not consider the abusive behaviors to be abuse. Perceptions of abuse were relatively stable across the 5 types of abuse examined (range: 25%–27%). Perceptions of the 15 abusive behaviors only varied due to older age in 3 instances, differences were sometimes between older adults and adults and sometimes children. Regression analyses showed increased ageism to be predictive of disagreement that behaviors were abusive in the older age group, explaining 8%–14% of the variance in perception. Regression models were not significant in the adult or child groups.

Discussion

Results raise serious concern about the perception of abuse toward older adults. Future studies should investigate the reasons for such perceptions and other contributing factors in order to identify effective mechanisms for change.
Gibberellin promotes theanine synthesis by relieving the inhibition of CsWRKY71 on CsTSI in tea plant (Camellia sinensis)
Authors: Xiang Fen , Su Yi , Zhou Lingyun , Dai Cuiting , Jin Xuan , Liu Hongyan , Luo Weigui , Yang Wenbo , Li Wei
Published: November 2024

Theanine is a crucial indicator of tea quality, and its significance is closely tied to the economic value of tea. There have been many reports on the regulation mechanism of theanine synthesis and accumulation, but the mechanism by which gibberellin regulates theanine synthesis in tea plants is poorly understood. Previous studies have shown that the content of theanine experiences significant changes in the growth stages of tea shoots, displaying a strong correlation with gibberellin. This study confirmed that gibberellin significantly promoted the expression of the major gene of theanine synthesis, known as CsTSI. Additionally, the study identified CsWRKY71 as a transcription factor that mediated the regulation by gibberellin of theanine synthesis in tea plants. CsWRKY71 was localized in the nucleus and had a typical WRKY domain. It was a member of subclass IIC and its expression was significantly suppressed following exogenous GA3 treatment. Further assays, such as the electrophoretic mobility shift assay, dual luciferase and asODN (antisense oligodeoxynucleotide) interference, demonstrated that CsWRKY71 significantly interacted with the promoter of CsTSI, which inhibited theanine synthesis by binding to the cis-acting element (C/T)TGAC(T/C) of the CsTSI promoter. Overall, the addition of exogenous gibberellin alleviated the inhibition of CsTSI by down-regulating the expression of CsWRKY71, ultimately facilitating the rapid biosynthesis of theanine. This study elucidated the molecular mechanism of CsWRKY71-mediated gibberellin regulation of theanine synthesis in tea plant. The findings not only enhance our understanding of the regulatory processes involved in theanine synthesis in tea plants, but also provide important references for maintaining the characteristics of high theanine in the tea plant.
Evidence of a pelagic nursery area for phyllosomas of the scyllarid lobster Acantharctus ornatus (Holthuis, 1960) (Decapoda: Achelata: Scyllaridae) in a coastal bight in South Africa
Authors: Groeneveld Johan C , Porter Sean N , Govender Ashrenee
Published: November 2024

Lobster phyllosoma larvae collected during surveys over the continental shelf of eastern South Africa (southwestern Indian Ocean) were analysed to determine the role of the KwaZulu-Natal (KZN) Bight as a pelagic nursery area. Surface waters in the shallow bight and further offshore, between the 20- and 1,000-m depth contours, were sampled with plankton nets in 2018 to 2023. Phyllosomas were absent from 87.9% of 257 tows, with high variability in the remaining tows indicating a patchy distribution with abundance hotspots. Phyllosomas of four scyllarid and three palinurid species were found among 311 captured specimens. The scyllarid Acantharctus ornatus (Holthuis, 1960) was the most abundant, constituting 94.9% of the phyllosomas caught, with all nine larval stages (I–IX) present. Phylogenetic analysis using the COI and 16S rDNA gene markers confirmed that previously undescribed early larval stages in samples belonged to A. ornatus. Most A. ornatus phyllosomas were caught at shallow-bight stations, with catch rates declining steeply to the north and south of the bight and when bottom depth exceeded 100 m. Season and sampling station (nested within cross-shelf transect) were significant variables in explaining phyllosoma abundance. We provide evidence that the KZN Bight serves as a pelagic nursery area for A. ornatus phyllosoma larvae at all developmental stages, but not for other lobster species with known adult populations in the region.
A longitudinal examination of collaboration diversity among communication scholars: 1990–2023
Authors: Xu Shan , Jitkajornwanich Kulsawasd , David Prabu , Park Hye-jung , Zhao Yani , Adu Jeffery , Chumthong Thanathip
Published: November 2024

This study examines racial diversity in co-authorship in articles published in communication journals and its association with citations accrued over time. We analyzed 76,217 publications from 73 communication journals, spanning from 1990 to 2023, with a focus on racial diversity in authorship as an indicator of collaboration diversity. Our results reveal that diversity is positively associated with the number of citations received, with this positive effect increasing over time. In addition, non-White lead authors collaborated more diversely, whereas White authors exhibited a faster increase in collaboration diversity over the years. Furthermore, the positive association between collaboration diversity and citations was more pronounced when the lead author was non-White than when White. Additional analyses show a concerning disparity: While non-White first authors are equally likely as their White counterparts to publish in top journals, they receive significantly fewer citations.
Bare singular names and genericity
Authors: Gasparri Luca
Published: November 2024

Predicativists hold that proper names are count nouns with a predicative meaning, and treat bare singular names as predicative DPs headed by an unpronounced definite. However, bare singular names exhibit differences in grammatical behavior from ordinary definite singulars. One difference, it has been argued, is that while ordinary definite singulars can be interpreted generically, bare singular names cannot. This is not right: bare singular names can have generic uses. I present the evidence and offer an argument that generics with bare singular names are good news for predicativists.
Primary division of annular pancreas: a surgical technique
Authors: Lim Kai-Zheong , Lee Alice , Croagh Daniel
Published: November 2024

The authors presented a case of duodenal obstruction in a 61-year-old man, resulting from an annular pancreas diagnosed on imaging (computed tomography, magnetic resonance cholangiopancreatography, and endoscopic ultrasound). The patient underwent a diagnostic laparoscopy. Intraoperatively, given a straightforward appearance and anatomy of the annular pancreas overlying the second part of the duodenum, and due to extensive adhesions in the abdomen, a primary division of the annular pancreas was performed, instead of a bypass procedure such as gastrojejunostomy. He had some residual symptoms 1 week postoperatively which was treated with duodenal dilatation endoscopically. On review and follow-up at 1 year, he has remained well with resolution of symptoms, supported by radiological improvement on a computed tomography performed at 4 months post-operatively. We believe this approach has resulted in less morbidity and a shorter period of recovery as compared to a bypass procedure and represents a reasonable therapeutic option for annular pancreas.
Chemical evolution of an evaporating lava pool
Authors: Curry Alfred , Mohanty Subhanjoy , Owen James E
Published: November 2024

Many known rocky exoplanets are so highly irradiated that their dayside surfaces are molten, and ‘silicate atmospheres’, composed of rock-forming elements, are generated above these lava pools. The compositions of these ‘lava planet’ atmospheres are of great interest because they must be linked to the composition of the underlying rocky interiors. It may be possible to investigate these atmospheres, either by detecting them directly via emission spectroscopy or by observing the dust tails which trail the low-mass ‘catastrophically evaporating planets’. In this work, we develop a simple chemical model of the lava pool–atmosphere system under mass-loss, to study its evolution. Mass-loss can occur both into space and from the day to the nightside. We show that the system reaches a steady state, where the material in the escaping atmosphere has the same composition as that melted into the lava pool from the mantle. We show that the catastrophically evaporating planets are likely to be in this evolved state. This means that the composition of their dust tails is likely to be a direct trace of the composition of the mantle material that is melted into the lava pool. We further show that, due to the strength of day-to-nightside atmospheric transport, this evolved state may even apply to relatively high-mass planets ($\gtrsim 1\mathrm \,{M}_{\oplus }$). Moreover, the low pressure of evolved atmospheres implies that non-detections may not be due to the total lack of an atmosphere. Both conclusions are important for the interpretation of future observations.
Arkenstone – II. A model for unresolved cool clouds entrained in galactic winds in cosmological simulations
Authors: Smith Matthew C , Fielding Drummond B , Bryan Greg L , Bennett Jake S , Kim Chang-Goo , Ostriker Eve C , Somerville Rachel S
Published: November 2024

Arkenstone is a new scheme that allows multiphase, stellar feedback-driven winds to be included in coarse resolution cosmological simulations. The evolution of galactic winds and their subsequent impact on the circumgalactic medium are altered by exchanges of mass, energy, momentum, and metals between their component phases. These exchanges are governed by complex, small-scale physical processes that cannot be resolved in cosmological simulations. In this second presentation paper, we describe Arkenstone’s novel cloud particle approach for modelling unresolvable cool clouds entrained in hot, fast winds. This general framework allows models of the cloud–wind interaction, derived from state-of-the-art high-resolution simulations, to be applied in a large-scale context. In this work, we adopt a cloud evolution model that captures simultaneous cloud mass loss to and gain from the ambient hot phase via turbulent mixing and radiative cooling, respectively. We demonstrate the scheme using non-cosmological idealized simulations of a galaxy with a realistic circumgalactic medium component, using the arepo code. We show that the ability of a high-specific energy wind component to perform preventative feedback may be limited by heavy loading of cool clouds coupled into it. We demonstrate that the diverging evolution of clouds of initially differing masses leads to a complex velocity field for the cool phase and a cloud mass function that varies both spatially and temporally in a non-trivial manner. These latter two phenomena can manifest in the simulation because of our choice of a Lagrangian discretization of the cloud population, in contrast to other proposed schemes.
hyenas: X-ray bubbles and cavities in the intragroup medium
Authors: Jennings Fred J , Babul Arif , Davé Romeel , Cui Weiguang , Rennehan Douglas
Published: November 2024

We investigate the role of the simba feedback model on the structure of the intragroup medium (IGrM) in the new hyenas suite of cutting-edge cosmological zoom-in simulations. Using 34 high-resolution zooms of haloes spanning from $10^{13}-10^{14}$${\rm M_\odot}$ at $z=0.286$, we follow haloes for 700 Myr, over several major active galactic nuclei (AGNs) jet feedback events. We use the moxha package to generate mock Chandra X-ray observations, as well as predictive mocks for the upcoming LEM mission, identifying many feedback-generated features such as cavities, shock-fronts, and hot-spots, closely mimicking real observations. Our sample comprises 105 snapshots with identified cavities, 50 with single bubbles, and 55 with two, and spans three orders of magnitude in observed cavity enthalpies, from $10^{41}-10^{44}$ erg s−1. Comparing semimajor axis length, midpoint radius, and eccentricity to a matched sample of observations, we find good agreement in cavity dimensions with real catalogues. We estimate cavity power from our mock maps following observational procedures, showing that this is typically more than enough to offset halo cooling, particularly in low-mass haloes, where we match the observed excess in energy relative to cooling. Bubble enthalpy as measured with the usual midpoint pressure typically exceeds the energy released by the most recent jet event, hinting that the mechanical work is done predominantly at a lower pressure against the IGrM. We demonstrate for the first time that X-ray cavities are observable in a modern large-scale simulation suite and discuss the use of realistic cavity mock observations as new halo-scale constraints on feedback models in cosmological simulations.
Serendipitous observation of a white dwarf companion to a JWST/MIRI coronagraphic calibrator
Authors: Venner Alexander , Limbach Mary Anne , Mâlin Mathilde , Blouin Simon , Boccaletti Anthony , Pearce Logan A
Published: November 2024

We present the unplanned detection of a white dwarf companion to the star HD 218261 in mid-infrared (10–16 $\mu$m) observations with JWST/MIRI. This star was observed as a calibrator for coronagraphic observations of the exoplanet host HR 8799. HD 218261 B has only previously been detected by Gaia, and only in visible light. We confidently detect the companion in the mid-infrared, where it is less luminous than the primary by a factor of ${\sim} 10^4$. The visible and mid-infrared photometry are consistent with a white dwarf of $T_\text{eff}\approx 10000$ K, $M\approx 0.8~\mathrm{ M}_\odot$, though observation of its optical spectrum is required to precisely constrain its physical parameters. These results demonstrate that precise mid-infrared photometry of white dwarf companions to bright stars can be obtained with MIRI, opening up new possibilities for studying white dwarfs in close binaries.
Formation mechanism of iron–catechol complexes in the colored periostracum of Corbicula spp.
Authors: Takemoto Kuniko , Murakami Masataka , Ueno Yoshihiro , Bamba Daiya , Yamagishi Hirona
Published: November 2024

The shell color of Corbicula clams, which are globally distributed, is roughly divided into yellowish and blackish depending on the environmental conditions of the sediment. The formation of an iron–L-3,4-dihydroxyphenylalanine (DOPA) complex in a thin organic layer, called the periostracum, on a calcareous layer causes the blackening of the clamshell. However, the iron–DOPA complex formation mechanism is unclear. To reveal how the iron is transported from the aquatic environment to the periostracum, cross-sectional analyses of the shell were conducted using an electron probe microanalyzer and Raman spectroscopy to investigate the distribution and structure of iron in the shell. Iron was only present in the periostracum, excluding deposition, and all iron was in the form of an iron–DOPA complex. Attenuated total reflection infrared spectroscopy and oxygen K-edge X-ray absorption fine structure spectroscopy revealed that the molecular structure of the native periostracum is independent of shell color. These results indicate that dissolved iron–organic complexes diffuse from the aqueous environment to the periostracum, forming iron–DOPA complex through ligand exchange. Because the iron–DOPA complex color depends on the pH, the shell color can serve as a historical indicator of the shell's growth environment.