bluuebunny/crossref_metadata_2025 huggingface dataset:
AskBeacon—Performing genomic data exchange and analytics with natural language
Authors: Wickramarachchi Anuradha , Tonni Shakila , Majumdar Sonali , Karimi Sarvnaz , Kõks Sulev , Hosking Brendan , Rambla Jordi , Twine Natalie A , Jain Yatish , Bauer Denis C
Published: February 2025

Motivation

Enabling clinicians and researchers to directly interact with global genomic data resources by removing technological barriers is vital for medical genomics. AskBeacon enables Large Language Models to be applied to securely shared cohorts via the GA4GH Beacon protocol. By simply “asking” Beacon, actionable insights can be gained, analyzed and made publication-ready.

Results

In the Parkinson's Progression Markers Initiative (PPMI) we use natural language to ask whether the sex-differences observed in Parkinson's disease are due to X-linked or autosomal markers. AskBeacon returns a publication-ready visualization showing that for PPMI the autosomal marker occurred 1.4 times more often in males with Parkinson’s disease than females, compared to no differences for the X-linked marker. We evaluate commercial and open-weight LLM models, as well as different architectures to identify the best strategy for translating research questions to Beacon queries. AskBeacon implements extensive safety guardrails to ensure that genomic data is not exposed to the LLM directly, and that generated code for data extraction, analysis and visualization process is sanitized and hallucination resistant, so data cannot be leaked or falsified.

Availability

AskBeacon is available at https://github.com/aehrc/AskBeacon.

Supplementary information

Supplementary data are available at Bioinformatics online.
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow
Authors: Hamraoui Ali , Jourdren Laurent , Thomas-Chollier Morgane
Published: February 2025

Motivation

The combination of long-read sequencing technologies like Oxford Nanopore with single-cell RNA sequencing (scRNAseq) assays enables the detailed exploration of transcriptomic complexity, including isoform detection and quantification, by capturing full-length cDNAs. However, challenges remain, including the lack of advanced simulation tools that can effectively mimic the unique complexities of scRNAseq long-read datasets. Such tools are essential for the evaluation and optimization of isoform detection methods dedicated to single-cell long read studies.

Results

We developed AsaruSim, a workflow that simulates synthetic single-cell long-read Nanopore datasets, closely mimicking real experimental data. AsaruSim employs a multi-step process that includes the creation of a synthetic UMI count matrix, generation of perfect reads, optional PCR amplification, introduction of sequencing errors, and comprehensive quality control reporting. Applied to a dataset of human peripheral blood mononuclear cells (PBMCs), AsaruSim accurately reproduced experimental read characteristics.

Availability

The source code and full documentation are available at: https://github.com/GenomiqueENS/AsaruSim.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Caring Encounters Guiding Framework: A Narrative Inquiry-Informed Innovative Model for Navigating Diversity
Authors: Braganza Morgan E , Hodge David R
Published: February 2025

Countries worldwide are characterised by increasing diversity. In Western societies, social diversification has contributed to escalating tension amongst people holding different worldviews. The emergence of what some have called superdiverse societies has led to calls for new models to assist social workers navigate differences. In response, the present study developed an innovative model—the Caring Encounters Guiding Framework—to successfully navigate difficult interactions. To develop this model, narrative inquiry was used with a sample of thirty-two individuals who self-identified as members of diverse groups. Analysis produced a preliminary Framework comprising three interconnected elements: Context, Core Issues and Prescriptions. The Framework provides guiding principles and processes for transversing interactions in both direct practice and educational settings. Included amongst these are considering the context in which interactions occur, attending to how differences are perceived and discussed, and using flexibility in approaching each interaction. Implementing the strategies embedded in this Framework positions social workers to interact with each individual in a caring and sensitive manner that respects their unique differences and cultural backgrounds.
A scoping review of birth alerts: A Canadian context
Authors: Elke Danielle , Choate Peter , Tortorelli Christina
Published: February 2025

This scoping review examines the history and application of birth alerts in Canada, from social work, legal, policy, and social justice lenses. In Canada, child welfare authorities developed a practice commonly known as birth alerts. This evolved across the country in an uneven fashion but has certainly been active since the early 2000s. There are many criticisms including causing undue trauma with children and families and disrupting early attachment as well as focus on Indigenous women in Canada as an example of racial bias (Doenmez et al. 2022). Since the release of the National Inquiry into Missing and Murdered Women and Girls (2019) report, provinces and territories have ended the practice. Literature reviewed examine birth alerts, pre-birth child welfare involvement and child welfare involvement at the birth of a child. Primarily, Canadian sources are used; however, countries with similar child welfare structures such as Australia, the UK, and the USA are considered. Studies using various methods have been included: qualitative, quantitative, mixed-method, systematic reviews, grey literature, and case law. This review uses the JBI Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methods for scoping reviews (Peters et al. 2015).
The role of meningioma integrated molecular profiling to improve patient management and disclose novel therapeutic targets
Authors: Bertero Luca , Padovan Marta , Giuseppe Lombardi
Published: February 2025

This scientific commentary refers to ‘Integrating genome-wide association studies and transcriptomics prioritizes drug targets for meningioma’, by  Liao et al. (https://doi.org/10.1093/braincomms/fcaf053).
Association between amyloid-β42 levels and neuropsychiatric symptoms in Alzheimer’s disease trials
Authors: Abanto Jesus Thomas , Dwivedi Alok K , Imbimbo Bruno P , Espay Alberto J
Published: February 2025

Research on how Alzheimer’s disease drugs impact neuropsychiatric symptoms is limited. Given the link between changes in cerebrospinal fluid (CSF) amyloid-β42 (Aβ42) levels and cognitive and clinical outcomes after anti-Aβ treatments, we hypothesized a similar association exists with neuropsychiatric symptoms.

We conducted a meta-analysis of anti-Aβ drugs clinical trials to evaluate whether the changes in cerebrospinal Aβ42 levels are associated with neuropsychiatric symptoms, as measured by the Neuropsychiatric Inventory and if any such effect is mediated by changes in cognitive performance, as measured by the Mini-Mental State Examination.

Data from 10 trials involving 10,746 Alzheimer’s disease patients were included. Decreases in Aβ42 levels were associated with worsening Neuropsychiatric Inventory scores (Regression Coefficient [RC]: -0.68; 95% Confidence Interval [CI]: -1.07 to -0.29; P = 0.002), and this association persisted after adjusting for Mini-Mental State Examination. Sensitivity analyses confirmed the robustness of these findings.

Changes in CSF Aβ42 levels are inversely and independently associated with the frequency and severity of neuropsychiatric symptoms in anti-Aβ trials, suggesting a potential role of Aβ42 in modulating neuropsychiatric symptoms in Alzheimer’s disease.
Humoral and cellular immunogenicity of a fourth dose BNT162b2 in children with chronic kidney diseases
Authors: Chan Jeffery C H , Chan Eugene Yu-Hin , Cheng Samuel M S , Leung Daniel , Ho Fanny Tsz-Wai , Tong Pak-Chiu , Lai Wai-Ming , Lee Matthew H L , Chim Stella , Tsang Leo C H , Kwan Tsz-Chun , Cheuk Yin Celeste , Wang Manni , Wong Howard H W , Lee Amos M T , Li Wing Yan , Chan Sau Man , Tam Issan Y S , Lam Jennifer H Y , Zhang Kaiyue , Tu Wenwei , Peiris Malik , Duque Jaime S Rosa , Lau Yu Lung , Ma Alison Lap-Tak
Published: February 2025

Background

Children with chronic kidney diseases (CKD) are at risk of severe complications after SARS-CoV-2 infection and are recommended to receive vaccine boosters. Although COVID-19 boosters are effective in providing immune responses among healthy children, data on the use of a fourth dose among children with CKD are limited.

Methods

We prospectively investigated the immunogenicity and safety of a fourth dose of BNT162b2 in children with CKD. Dosages were 0.1 mL and 0.3 mL for children aged 5–11 years and 11–18 years, respectively. Humoral and cellular immunogenicity was assessed at pre-dose 4, and 1- and 6-month post-dose 4.

Results

Twenty-one children, with a median age of 14.0 years, were included for evaluation. A fourth dose of BNT162b2 elicited significant increases in humoral spike receptor-binding domain IgG levels and T-cell responses. Antibody responses were significantly lower among kidney transplant recipients or children receiving calcineurin inhibitors than other CKD children at 1-month post-dose 4. Breakthrough COVID-19 occurred in three children after the fourth dose, and one was hospitalized. One child developed mild gross hematuria 1 day after the fourth dose, which spontaneously resolved. The overall safety profile was acceptable.

Conclusions

A fourth dose of BNT162b2 was immunogenic and safe in children with CKD.
Enemy dispersal drives the diversity loss of bacterial victim populations at diversity cold spots
Authors: Chu Xiao-Lin
Published: February 2025

Dispersal between heterogenous habitats is a major determinant of population diversification, and may often introduce new morphotypes in habitats where population diversity is low. Natural enemies are also key factors affecting the diversification of victim populations. Co-dispersal of enemies may induce local diversity loss at diversity cold spots as enemies from diversity hots pots are often more efficient in predation. Here, we experimentally tested this hypothesis using a model microbial system: Pseudomonas fluorescens and its lytic phage. The ancestral bacterium diversified at three resource levels across eight temperature gradients in the presence and absence of phages. Bacteria diversified into more morphotypes at higher temperatures and higher resource levels when phages are absent, and dispersal increased population local diversity at low-diversity habitats. The presence of phages removed the differences in morphological diversity among different temperatures or resource levels. In addition, the co-dispersal of enemies caused higher morphotype loss at lower-quality habitats where the local bacteria are of lower resistance. The simultaneous dispersal of enemies and victims may have crucial consequences for population persistence in edge habitats.
Multi-omics analysis of the correlation between surface microbiome and metabolome in Saccharina latissima (Laminariales, Phaeophyceae)
Authors: Adouane Emilie , Hubas Cédric , Leblanc Catherine , Lami Raphaël , Prado Soizic
Published: February 2025

The microbiome of Saccharina latissima, an important brown macroalgal species in Europe, significantly influences its health, fitness, and pathogens resistance. Yet, comprehensive studies on the diversity and function of microbial communities (bacteria, eukaryotes, and fungi) associated with this species are lacking. Using metabarcoding, we investigated the epimicrobiota of S. latissima and correlated microbial diversity with metabolomic patterns (LC-MS/MS). Specific epibacterial and eukaryotic communities inhabit the S. latissima surface, alongside a core microbiota, while fungal communities show lower and more heterogeneous diversity. Metabolomic analysis revealed a large diversity of mass features, including putatively annotated fatty acids, amino derivatives, amino acids, and naphthofurans. Multiple-factor analysis linked microbial diversity with surface metabolome variations, driven mainly by fungi and bacteria. Two taxa groups were identified: one associated with bacterial consortia and the other with fungal consortia, each correlated with specific metabolites. This study demonstrated a core bacterial and eukaryotic microbiota associated with a core metabolome and highlighted interindividual variations. Annotating the surface metabolome using Natural Products databases suggested numerous metabolites potentially involved in inter-species chemical interactions. Our findings establish a link between microbial community structure and function, identifying two microbial consortia potentially involved in the chemical defense of S. latissima.
Associations between pre-widowhood psychological resilience and subsequent depressive symptom recovery following spousal loss among men and women
Authors: Chauhan Shekhar , Carr Dawn C , Taylor Miles
Published: February 2025

Background and Objectives

Most older widowed men and women experience elevated depressive symptoms after spousal loss, and many recover to pre-widowhood levels over time. However, not all widows return to pre-loss mental health, and recovery may differ by gender. Pre-widowhood psychological resilience (PR) has been shown to influence these effects. This study evaluates changes in depressive symptoms for older men and women to determine how PR shapes acute and long-term depressive symptom responses to spousal loss.

Research Design and Methods

Using longitudinal Health and Retirement Study data, we evaluate changes in depressive symptoms from baseline PR pre-widowhood to (1) the first study wave in which individuals report widowhood (acute effects) and (2) the second wave after reporting widowhood (recovery period), for men and for women. We use inverse probability weighted regression models, comparing new widows with their continuously married counterparts.

Results

Both widowed men and women experienced increased depressive symptoms in the acute period following spousal loss regardless of PR level. However, moderate to high levels of PR for men and high PR for women predicted recovery to pre-widowhood depressive symptoms two years later. High PR was also associated with fewer depressive symptoms over time among continuously married men and women.

Discussion and Implications

Results suggest interventions that bolster PR preceding spousal loss could enhance likelihood of recovery following widowhood for both men and women and may also provide protective effects regarding overall depressive symptoms among married individuals over time.
Seismic wavefield injection based on interface discontinuity: Theory and numerical implementation based upon the spectral-element method
Authors: Liu Tianshi , Du Nanqiao , Lei Ting , Wang Kai , He Bin , Tong Ping , Grasselli Giovanni , Liu Qinya
Published: February 2025

In seismology, wavefield injection refers to the propagation of seismic waves generated by remote sources into local domains bounded by enclosed surfaces. The simulations of wavefield injection, primarily focused on the interaction between incoming seismic waves and local structures, are key to earthquake hazard modeling and full-waveform seismic tomography using tele-seismic waves. In this paper, we show that simulating wavefield injection is equivalent to solving the wave equation subject to interface discontinuity conditions. To provide a general framework to study wavefield injection, we formally define the interface discontinuity problem, and discuss its representation theorem and uniqueness. We also develop an efficient interface-discontinuity-based numerical algorithm to solve the wavefield injection problem through implementations of spectral-element methods, and show with numerical examples that wavefield injection can be accurately simulated at different scales with this algorithm. Under this framework, we draw connections with previously proposed wavefield injection algorithms/hybrid methods, and clarify several theoretical questions on wavefield injection from previous research. We demonstrate the efficiency and accuracy of our approach through wavefield injection examples at local and continental scales. Furthermore, we illustrate the applicability of the interface discontinuity approach to performing kinematic fault simulations through an numerical example.
A decade of the fast-varying ionospheric and magnetospheric magnetic fields from ground and multi-satellite observations
Authors: Min Jingtao , Grayver Alexander
Published: February 2025

The time-varying geomagnetic field is a superposition of contributions from multiple internal and external current systems. A major source of geomagnetic variations at periods less than a few years are current systems external to the solid Earth, namely the ionospheric and magnetospheric currents, as well as associated induced currents. The separation of these three sources is mathematically underdetermined using either ground or satellite measurements alone, but becomes tractable when the two datasets are combined. Based on this concept, we developed a new geomagnetic field modelling approach that allows us to simultaneously characterise the mid-latitude ionospheric, magnetospheric and the internal induced magnetic fields using ground and satellite observations for all local times and magnetic conditions, and without prescribing any harmonic behaviour on these current systems in time, as is typical in other models. By applying this new method to a 10-year dataset of ground observatory and multi-satellite measurements from 2014 to 2023, we obtained the time series of the spherical harmonic coefficients of the ionospheric, magnetospheric and induced fields. These new time series allow the study of complex non-periodic dynamics of the external magnetic fields during global geomagnetic storms, as well as periodicities in the magnetospheric coefficients linked to solar activities and periodic ionospheric magnetic fields linked to lunar daily variations, contributing to a more complete picture of the dynamics of the external currents and magnetosphere-ionosphere interactions, and facilitating more accurate space weather nowcast and forecast. Finally, the new approach allows for a better characterisation of internal induced field sources, leading to higher quality electromagnetic transfer functions.
The stability of frictional sliding on dip-slip and finite length faults
Authors: Skarbek Rob M
Published: February 2025

This paper examines the linear stability of sliding on faults embedded in a 2D elastic medium that obey rate and state friction and have a finite length and/or are near a traction-free surface. Results are obtained using a numerical technique that allows for analysis of systems with geometrical complexity and heterogeneous material properties; however only systems with homogeneous frictional and material properties are examined. Some analytical results are also obtained for the special case of a fault that is parallel to a traction-free surface. For velocity-weakening faults with finite length, there is a critical fault length L* for unstable sliding that is analogous to the critical wavelength h* that is usually derived from infinite fault systems. Faults longer than L* are linearly unstable to perturbations of any length. On vertical strike-slip faults or faults in a full-space L* ≈ h*/e, where e is Euler’s number. For dip-slip faults near a traction-free surface L* ≤ h*/e and is a function of dip angle β, burial depth d of the fault’s up-dip edge, and friction coefficient. In particular, L* is at least an order of magnitude smaller than h* on shallowly dipping (β < 10○) faults that intersect the traction-free surface. Additionally, L* ≈ h*/e on dip-slip faults with burial depths d ≥ h*. For sliding systems that can be treated as a thin layer, such as landslides, glaciers, or ice streams, L* = h*/2. Finally, conditions are established for unstable sliding on infinitely-long, velocity-strengthening faults that are parallel to a traction-free surface.
Improving passive reflection seismic imaging in complex geological settings through site effect reduction: application to Krafla volcano, Iceland
Authors: Maass Regina , Li Ka Lok , Bean Christopher J
Published: February 2025

Reflection imaging at volcanoes presents significant challenges due to the highly heterogeneous subsurface, which generates complex wavefields characterized by substantial wave scattering. These scattered waves obscure coherent energy, such as reflections from geological structures in the subsurface. In this study, we develop processing strategies to address the limitations of high-frequency (5-20 Hz) passive reflection imaging at Krafla, a volcanic caldera in NE Iceland. Krafla is among the few locations worldwide where magma has been encountered at 2.1 km depth when drilling the IDDP1 borehole. We analyze over 300 local microearthquakes and industrial noise recorded during five weeks in the summer of 2022. We show that wavefields lack coherency even between stations spaced at 30-meter intervals due to the dominance of site effects beneath the stations. However, data coherency improves in the common-station domain, where different earthquakes recorded by a fixed station are analyzed, thereby stabilizing the site effect. Spectral analyses in this domain reveal that site effects are partly due to resonances at the stations, likely caused by lava flows and cavities in the heterogeneous near-surface. By constructing a resonance removal filter, we successfully deconvolve resonance effects from the data, revealing previously masked coherent energy. We further reduce site effects by applying linear stacking of clustered earthquake traces and non-linear amplitude weighting. Our approach significantly enhances coherency between stations and enables the identification of reflections in microearthquakes likely originating from the known magma-rock interface beneath the IDDP1 borehole.
MS-based Solutions for Single Cell Proteomics
Authors: Li Siqi , Li Shuwei , Liu Siqi , Ren Yan
Published: February 2025

Mass spectrometry-based single cell proteomics (MS-SCP) is attracting tremendous attention because it is now technically feasible to quantify thousands of proteins in minute samples. Since protein amplification is still not possible, technological improvements in MS-SCP focus on minimizing sample loss and increasing throughput, resolution, and sensitivity, as well as achieving the measurement depth, accuracy, and stability as bulk samples. Major advances in MS-SCP have facilitated its use in biological and even medical applications. Here, we review the key advancements in MS-SCP technology and discuss the strategies of the classic proteomics workflow to improve MS-SCP analysis from single cell isolation, sample preparation and liquid chromatography separation to MS data acquisition and analysis. The review will provide an overall understanding of the development and application of MS-SCP and inspire more novel ideas regarding the innovation of MS-SCP technology.
Synergistic effects of memantine and alpha7 nicotinic acetylcholine receptor agonist PHA-543613 to improve memory of aged rats
Authors: Bruszt Nóra , Bali Zsolt Kristóf , Nagy Lili Veronika , Bodó Kornélia , Engelmann Péter , Hernádi István
Published: February 2025

Background

Combination treatments based on pharmacological interactions at α7 nicotinic acetylcholine receptors (nAChR) are promising therapeutic approaches for neurocognitive disorders.

Methods

Here, we tested the cognitive efficacy of combinations of memantine with an α7 nAChR-selective agonist (PHA-543613) in naturally aged rats. Age-related changes in the expression of some key genes and proteins were also measured using quantitative PCR and ELISA.

Results

Aged rats showed marked cognitive decline in the novel object recognition test, and they also exhibited cholinergic changes such as mRNA upregulation of α7 nAChRs. Upregulation of interleukin-1β, MIP-1α, CX3CL1, ICAM-1 and CNTF mRNA were also detected in aged rats. Combination treatment of memantine and PHA-543613 successfully alleviated the age-related decline of recognition memory of rats by exceeding the effects of the corresponding monotreatments.

Conclusions

Results indicate a positive interaction between memantine and PHA-543613, which also reflects a putative role of α7 nAChRs in the cognitive enhancer effects of memantine. These findings may facilitate the development of combination therapies for age-related neurocognitive disorders.
Why the International Criminal Court Should Apply Restorative Justice and Transitional Justice Principles to Improve the Impact of Its Criminal Trials on Societies around the World
Authors: Sarkin Jeremy Julian
Published: February 2025

Both restorative and transitional justice have increasingly been applied in transitional settings to overcome the insufficient role that criminal trials have played. Using restorative justice was supposedly incorporated into the International Criminal Court (ICC) processes to overcome the so-called justice versus peace dilemma, that is, the choice between punishment or contributing to peacebuilding and preventing their reoccurrence. However, this so-called absorption has been based on a mistaken appreciation of restorative justice. It has been reduced to a mere alternative to retributive justice and overlaps with the broader concept of transitional justice. It has, therefore, failed to reap restorative justice’s true potential. This article, using theoretical and empirical methodologies, argues for the reconceptualization of international criminal justice within the ICC’s framework to effectively integrate retributive and restorative proceedings and punishments. It contends that changes to ICC practice are needed concerning victim participation, reparations and guarantees of non-repetition. It maintains that the ICC should cooperate more with local justice and transitional justice processes to positively enhance the role of the Court and for victims to attain more truth and foster reconciliation. In that way, the ICC could be more effective in dealing with atrocious human rights violations, ensuring justice delivery, while promoting enduring peace and fostering reconciliation.
Actinomycetota Isolated from the sponge Hymeniacidon perlevis as a Source of Novel Compounds with Pharmacological Applications: Diversity, Bioactivity Screening, and Metabolomic Analysis
Authors: Fonseca Ana C , Ribeiro Inês , Girão Mariana , Regueiras Ana , Urbatzka Ralph , Leão Pedro , Carvalho Maria F
Published: February 2025

Aims

To combat health conditions, such as multi-resistant bacterial infections, cancer and metabolic diseases, new drugs need to be urgently found and, in this respect, marine Actinomycetota have a high potential to produce secondary metabolites with pharmacological importance. We aimed to study the cultivable Actinomycetota community associated with a marine sponge from the Portuguese coast, Hymeniacidon perlevis, and investigate the potential of the retrieved isolates to produce compounds with antimicrobial, anticancer and anti-obesity properties.

Methods and Results

The analysis of the 16S rRNA gene revealed 79 Actinomycetota isolates affiliated with twelve genera - Brachybacterium, Dietzia, Glutamicibacter Gordonia, Micrococcus, Micromonospora, Nocardia, Nocardiopsis, Paenoartrhobacter, Rhodococcus, Streptomyces and Tsukamurella, most of which affiliated with the genus Streptomyces. The screening of antimicrobial activity revealed 13 strains, all belonging to the Streptomyces genus, capable of inhibiting the growth of Candida albicans, Bacillus subtilis or Staphylococcus aureus. Forty-three extracts exhibited cytotoxic activity against at least one tested cell line (HepG2, HCT-116 and hCMEC-D3). Three extracts that were active against the two cancer cell lines tested, did not reduce the viability of the non-cancer endothelial cell line, hCMEC-D3. One Gordonia strain exhibited anti-obesity activity, revealed by its ability to reduce the neutral lipids in zebrafish larvae. Mass spectrometry-based dereplication analysis of active extracts identified several compounds associated with known Actinomycetota natural products. Nonetheless, five clusters contained metabolites that did not match any annotated natural products, suggesting they may represent new bioactive molecules.

Conclusions

This work contributed to increase the knowledge on the diversity and bioactive potential of Actinomycetota associated with H. perlevis.
Breed-specific heterosis for growth and carcass traits in 18 U.S. cattle breeds
Authors: Engle Bailey N , Thallman R Mark , Snelling Warren M , Wheeler Tommy L , Shackelford Steven D , King D Andy , Kuehn Larry A
Published: February 2025

Heterosis, or hybrid vigor, is traditionally defined as the advantage of crossbred progeny relative to the average performance of their purebred parents. This advantage is due to increased heterozygosity in these crosses, which increases phenotypic expression in traits influenced by non-additive gene action. These heterosis effects may vary depending on the breed of animals in the original cross; however, breed-specific estimates are difficult to obtain because of a lack of contemporary comparisons among crossbred and purebred cattle. The Germplasm Evaluation Program at the U.S. Meat Animal Research Center was designed to evaluate 18 of the most highly utilized beef breeds in the United States and enable contemporary comparisons among purebreds and their crosses. Therefore, the primary objective of this study was to quantify the differences in breed-specific heterosis for growth and carcass traits in these 18 U.S. beef breeds. Specific traits analyzed were direct and maternal birth weight, direct and maternal 205d adjusted weaning weight, 365d postweaning gain, marbling score, ribeye area, backfat thickness, and carcass weight. Specific heterosis effects were estimated using two different models: 1) a biological-group heterosis model where heterosis was estimated for crosses between British, Continental, and Brahman as breed groups, and 2) an average breed heterosis model where heterosis was estimated as the regression on average predicted breed heterozygosity arising from mating each of the 18 breeds to a randomly chosen animal in the population. Each model also included a random breed-specific cross effect for each pair of breeds. Biological-group heterosis, or the expected deviations from a purebred mean between all crosses of British-, Brahman-, and Continental-groups, was found for all traits (P < 0.0001), except marbling. The greatest increases in calf performance were estimated for crosses containing Brahman, especially for growth traits and maternal ability. Average breed-specific heterosis was also significant (P < 0.05) under the second model again for all traits except marbling and maternal birth weight. Again, the greatest increase in calf performance across a majority of traits was found to be the result of crosses with Brahman. These estimates may be used by breeders to make more informed crossbreeding decisions, and to tailor their choice of breeds to their specific production environment and breeding objectives.
Negative Pressure Wound Therapy and its Use in Burn Wounds: An Updated Systematic Review
Authors: Kuromaru Yuki , Won Paul , Madrigal Paloma , Choe Deborah , Gillenwater T Justin
Published: February 2025

Negative pressure wound therapy (NPWT) is a form of wound coverage that involves negative pressure and a semi-occlusive membrane to manage wound closure. In burn care, NPWT are currently utilized as temporary dressings for large wounds, skin-grafted burn wounds, and as a dressing on dermal substitutes. Little is known regarding optimal roles and indications of NPWT in burn care. This systematic review better characterizes the role of NPWT in burn care and provides updated recommendations. A systematic review of PubMed and Cochrane databases was performed utilizing PRISMA guidelines. All peer-reviewed publications published any time through September 17, 2021 were included. Inclusion criteria consisted of studies containing a control group without NPWT, an intervention group with NPWT, and studies involving the use of NPTW in burn care. A total of 15 studies were analyzed, with a Risk of Bias (ROB) analysis performed to rate the quality of included studies. We find NPWT is superior to conventional dressings as a modality for skin grafting coverage, dressing on dermal substitutes, dressing on donor site wounds, and dressing on moderate to large burns. Outcomes such as length of hospitalization, length of wound healing, and rates of infections were improved in those treated with NPWT compared to conventional dressings. In conclusion, several clear benefits to utilizing NPWT have been defined for several modalities in burn care. However, further research with more robust controlled clinical trials is necessary to better quantify the role of NPWT in burn care and to better define parameters to optimize wound healing.
Indirect aggression and the North Atlantic Treaty
Authors: Rech Walter
Published: February 2025

Western diplomats and policymakers involved in the negotiations of the North Atlantic Treaty (NAT) in the late 1940s believed that the Soviet Union would not take the risk of launching an armed attack against the western bloc in the near future. Instead, the NAT negotiators were deeply worried about Soviet ‘indirect aggression’ in the form of political infiltration, interference, and subversion, that is, hybrid operations. The question arises of why the notion of indirect aggression was eventually dropped during the NAT negotiations, whereas Article 5 on armed attack became the core provision of the treaty. The article shows that there might have been sound reasons for not explicitly mentioning the notion of indirect aggression in the treaty at the time. With hindsight, however, the failure to come to an agreement on the need to counter indirect aggression has had repercussions on the development of NATO cooperation and intelligence sharing ever since. It partly explains the difficulties that still exist in strengthening genuine intelligence and security collaboration for the purpose of preventing and countering hybrid warfare.
The legislative reform’s great designs
Authors: Folliard-Monguiral Arnaud , Rogers David
Published: February 2025

Design law has undergone a major reform after more than 20 years of existence, with the publication of Directive 2024/2823 of 23 October 2024 on the legal protection of designs and Regulation 2024/2822 of 23 October 2024 amending Council Regulation (EC) No 6/2002 on Community designs and repealing Commission Regulation (EC) No 2246/2002 [2024] OJ L2024/2822. The purpose of this Practice Point is to provide a quick overview of the most significant changes brought by the Design Legislative Reform Package to the existing legal framework. The contribution has a practical bias and is aimed at readers who wish rapidly to find the key amendments to both the recast Directive on the legal protection of designs and the amending Regulation on EU designs. The Design Legislative Reform Package seeks inter alia to broaden both the definition of a ‘product’ and the ways in which designs can be represented; to liberalize the spare parts market; to provide for new exceptions to the exclusive right while extending its scope to ‘external transit’ and 3D printing; to prevent the appropriation of cultural heritage through abuse of the registration system and to provide for an optional cancellation procedure of national designs.
Age cohort definition and evidence of sexual dimorphism in the Southern Hairy-nosed Wombat (Lasiorhinus latifrons), a large Australian marsupial
Authors: Kleemann Shannon L , Taggart David A
Published: February 2025

The ability to reliably differentiate age cohorts and detect and quantify sexual dimorphism in wildlife species is crucial before performing many ecological and biological analyses, including population demographics and commonly used body condition indices. In many wildlife species, however, these analyses are limited by a lack of detailed and reliable data. We used a long-term data set (>30 years and >2,600 individuals) to establish a method to reliably differentiate juvenile, subadult, and adult southern hairy-nosed wombats (Lasiorhinus latifrons) and provide evidence of sexual dimorphism in this species. Adult and subadult males were separated primarily through measurements of head width and head length, based on measurements from confirmed adult males (n = 160). We found adult males to have significantly longer (P-value = 4.374e−16) and wider (P-value = 2.2e−16) heads than adult females and a significantly longer pes length (P-value = < 2.2e−16). This divergence appears to occur when subadult males are approaching adulthood. However, no difference in body weight or total body length was observed between the sexes. Using these data, we established approximate size ranges for wombats of all age cohorts to underpin future research on the impacts of rainfall and drought on body condition, breeding, recruitment, and survival in this semiarid dwelling species. This research also highlights the importance of separating the sexes for analyses involving body measurements even when the species does not display obvious dimorphism.
Alzheimer disease-associated tau post-translational modification mimics impact tau propagation and uptake
Authors: Dickson John R , Sobolewski Robert G R , Fernandes Analiese R , Cooper Joanna M , Fan Zhanyun , Chung Mirra , Donahue Cameron , Oakley Derek H , Strickland Dudley K , Hyman Bradley T
Published: February 2025

As Alzheimer disease (AD) progresses, pathological tau spreads by cell-to-cell propagation of tau. This study aims to elucidate the impact of AD-associated post-translational modifications of tau-on-tau propagation. Tau propagation reporter constructs distinguishing donor cells from recipient cells were developed, and additional constructs were made with tau residues mutated from serine or threonine to aspartate to mimic the negative charge of a phosphorylation and/or from lysine to glutamine to mimic the charge-neutralizing effect of acetylation. Flow cytometry was used to quantify donor and recipient cells. This revealed that the mutations generally tended to reduce tau propagation compared to wildtype tau. Recombinant tau containing either wildtype or posttranslational modification mimicking mutations were used to treat Chinese hamster ovary cells or human induced pluripotent stem cell-derived neurons to quantify tau uptake, revealing that the mutations generally resulted in reduced uptake compared to wildtype tau. Surface plasmon resonance revealed that the mutations had a reduced affinity for lipoprotein receptor-related protein 1 (LRP1), a tau uptake receptor, compared to wildtype tau. Overall, these results suggest that AD-associated posttranslational modification mimicking mutations reduce the cell-to-cell propagation of tau by reducing tau uptake by recipient cells, which may be in part due to reduced binding affinity to LRP1.
The Swiss cheese model of social cues: a theoretical perspective on the role of social context in shaping social media’s effect on adolescent well-being
Authors: Trekels Jolien , Telzer Eva H
Published: February 2025

Media effects research has observed significant diversity in the effects of social media on adolescent well-being, with outcomes ranging from positive to negative and, in some cases, neutral effects. In an effort to comprehend and elucidate this diversity, we have formulated The Swiss Cheese Model of Social Cues, a theoretical framework that systematically categorizes potential sources contributing to these variations. This dynamic model encompasses the complex layers of social cues present within platforms, the social environment, and individual (neuro)susceptibility, collectively shaping how social media influences the well-being of adolescents. The primary goal of this model is to enhance research by concurrently considering a broader range of individual difference factors, providing a comprehensive framework for investigations into the complex interplay of social context in social media effects.
‘The Savage of Civilisation’: Jack the Ripper and the Spectre of Colonialism in Late-Victorian Culture
Authors: Plater Michael
Published: February 2025

This essay examines the use of colonial and imperial narratives throughout late-Victorian press reportage of the infamous ‘Jack the Ripper’ crimes of 1888. It reveals how these press reports, with their vehement insistence that ‘no Englishman’ could have committed the crimes, tapped into, and reflected, dominant imperial attitudes towards race, colonialism, and English self-identity. These representations offered a fixed, idealized version of ‘Englishness’, one which focused on the supposedly civilized, cultivated, masculine ‘English’ self as a symbol of national identity and cultural evolution, with those ‘other’ races beyond Britain’s immediate borders cast as their primitive, bestial antithesis. However, in documenting these attitudes, my work also reveals the deep sense of instability, unease, anxiety, and insecurity that lay behind such representations, and the attendant fear that these concepts of the advanced English self were a kind of grand façade or self-delusion, masking deeper, more unpleasant, truths about late-Victorian culture and society. As such, my work reveals how the Ripper reportage exposed these contradictions and insecurities, undermining and challenging long-held assumptions about British progress and hegemony.
Pure Gravitational Wave Estimation of Hubble’s Constant using Neutron Star - Black Hole Mergers
Authors: Fung Leo W H , Broadhurst Tom , Smoot George F
Published: February 2025

It has been predicted before the first detection of such events by LIGO, that the gravitational wave (GW) emission from compact binary coalescence can be used to constrain the expansion rate of the universe. Here we show how H0 can be derived purely from the GW of neutron star-black hole (NSBH) mergers using a Bayesian Hierarchical inference framework. This method provides an estimate of H0 spanning the redshift range, z < 0.25 with current GW sensitivity and without the need for any afterglow detection. We utilise the inherent distribution of neutron star masses together with the NSBH waveform amplitude and frequency to estimate distance and redshift respectively, thereby measuring H0 for the NSBH events up to systematics and observational uncertainties. With the most updated observations, our first estimate is $H_0 = 96^{+44}_{-50}$ km s−1 Mpc−1 for the likely NSBH events GW190426 and GW200115 using the proof-of-concept analysis outlined in this work. Taking into account of realistic detectors response and sensitivity, we forecast that soon, with 10 more such NSBH events we can reach competitive precision of δH0/H0 ≲ 20 %. It is valuable to have a completely independent, both in terms observations and relevant physics, method of determining H0 as is emphasized by the current controversy on H0 and attempts to explain it invoking new physics.
Constraints on the active galactic nucleus and starburst activity of local ultraluminous infrared galaxies from a broad range of torus models
Authors: Varnava Charalambia , Efstathiou Andreas , Farrah Duncan , Rigopoulou Dimitra
Published: February 2025

In this paper we further explore the properties of the HERschel Ultra Luminous Infrared Galaxy Survey (HERUS) sample of 42 local ultraluminous infrared galaxies (ULIRGs) with our recently developed Bayesian spectral energy distribution (SED) fitting code SMART (Spectral energy distributions Markov chain Analysis with Radiative Transfer models). SMART fits SEDs exclusively with multicomponent radiative transfer models. Mid-infrared spectroscopy can be included in the fitting at a spectral resolution matched to that of the radiative transfer models. We fit the SEDs of the HERUS ULIRGs with four different models for the active galactic nucleus (AGN) torus, a starburst and a spheroidal galaxy model, to put constraints on the AGN fraction of the galaxies and their star formation rate (SFR). Two of the AGN torus models we explored are smooth and two are two-phase. We find that, in most cases, a smooth tapered AGN torus provides the best fit to the data. We also find that solutions with other torus models may predict AGN and total luminosities up to an order of magnitude or more lower, but very rarely higher than the best-fitting model. In contrast, we find that, with minor exceptions, the predicted SFR and stellar mass of the ULIRGs are generally robustly estimated irrespective of the assumed torus model. This is despite the fact that one of the AGN torus models we use assumes fluffy grains with high emissivity in the far-infrared and submillimetre, which could potentially reduce the contribution of a starburst at those wavelengths and reduce the SFR.
Stellar streams from black hole-rich star clusters
Authors: Roberts Daniel , Gieles Mark , Erkal Denis , Sanders Jason L
Published: February 2025

Nearly a hundred progenitor-less, thin stellar streams have been discovered in the Milky Way, thanks to Gaia and related surveys. Most streams are believed to have formed from star clusters and it was recently proposed that extended star clusters – rich in stellar-mass black holes (BHs) – are efficient in creating streams. To better understand the nature of stream progenitors, we quantify the differences between streams originating from star clusters with and without BHs using direct N-body models and a new model for the density profiles of streams based on time-dependent escape rates from clusters: the Quantifying Stream Growth (QSG) model. QSG facilitates the rapid exploration of parameter space and provides an analytic framework to understand the impact of different star cluster properties and escape conditions on the structure of streams. Using these models it is found that, compared to streams from BH-free clusters on the same orbit, streams of BH-rich clusters: (1) are approximately five times more massive; (2) have a peak density three times closer to the cluster 1 Gyr post-evaporation (for orbits of Galactocentric radius ≳ 10 kpc), and (3) have narrower peaks and more extended wings in their density profiles. We discuss other observable stream properties that are affected by the presence of BHs in their progenitor cluster, namely the width of the stream, its radial offset from the orbit, and the properties of the gap at the progenitor’s location. Our results provide a step towards using stellar streams to constrain the BH content of evaporated (globular) star clusters.
Lowest-mass X-ray selected AGNs in the Boötes Field
Authors: Purohit Rujuta A , Hickox Ryan C , Petter Grayson C
Published: February 2025

We present a multi-wavelength analysis of three candidate active galactic nuclei (AGNs) in low-mass galaxies in the Boötes field with the aim of improving constraints on the occupation fraction of low-mass black holes (BHs). Galaxies with low stellar masses (M⋆ < 109.5M⊙) are particularly interesting hosts for AGNs as they may contain BHs that have not grown significantly since the epoch of their formation in the early Universe. Using archival data from the Chandra X-ray Observatory, we find three X-ray luminous low-mass galaxies and assess whether they host AGNs. We find one of these sources to be variable in the X-ray and compute its X-ray light curve and spectrum. We compute the X-ray, mid-infrared, and [O III] luminosities and compare them to established AGN luminosity relationships in the literature. We then fit various star-forming, dust emission, and AGN templates to the spectral energy distributions (SEDs). The star formation rates estimated from the SED fits are unable to explain the observed X-ray luminosities of the candidates, providing more support for the presence of AGNs. By analysing the deviation from linear relationships between X-ray and mid-infrared luminosities, we find these systems to be obscured (with log NH[cm−2] ∼ 22.7, >25.0, and 24.4, respectively). We employ the scaling relationship between BH mass and stellar velocity dispersion to estimate the BH masses as ∼105 − 106M⊙ and accreting at Eddington ratios 10−2 < λEdd < 10−1.