bluuebunny/crossref_metadata_2025 huggingface dataset:
scMMAE: masked cross-attention network for single-cell multimodal omics fusion to enhance unimodal omics
Authors: Meng Dian , Feng Yu , Yuan Kaishen , Yu Zitong , Cao Qin , Cheng Lixin , Zheng Xubin
Published: January 2025

Multimodal omics provide deeper insight into the biological processes and cellular functions, especially transcriptomics and proteomics. Computational methods have been proposed for the integration of single-cell multimodal omics of transcriptomics and proteomics. However, existing methods primarily concentrate on the alignment of different omics, overlooking the unique information inherent in each omics type. Moreover, as the majority of single-cell cohorts only encompass one omics, it becomes critical to transfer the knowledge learnt from multimodal omics to enhance unimodal omics analysis. Therefore, we proposed a novel framework that leverages masked autoencoder with cross-attention mechanism, called scMMAE (single-cell multimodal masked autoencoder), to fuse multimodal omics and enhance unimodal omics analysis. scMMAE simultaneously captures both the shared features and the distinctive information of two single-cell omics modalities and transfers the knowledge to enhance single-cell transcriptome data. Comparative evaluations against benchmarking methods across various cohorts revealed a notable improvement, with an increase of up to 21% in the adjusted Rand index and up to 12% in normalized mutual information in the context of multimodal fusion. In the realm of unimodal omics, scMMAE demonstrated an overall enhancement of approximately 20% in the adjusted Rand index and nearly 10% in normalized mutual information. Other nine metrics, including the Fowlkes–Mallows index and silhouette coefficient, further underscored the high performance of scMMAE. Significantly, scMMAE exhibits an elevated level of proficiency in distinguishing between different cell types, particularly on CD4 and CD8 T cells. Availability and implementation: scMMAE source code at https://github.com/DM0815/scMMAE/.
Deconvolution of spatial transcriptomics data via graph contrastive learning and partial least square regression
Authors: Mo Yuanyuan , Liu Juan , Zhang Lihua
Published: January 2025

Deciphering the cellular abundance in spatial transcriptomics (ST) is crucial for revealing the spatial architecture of cellular heterogeneity within tissues. However, some of the current spatial sequencing technologies are in low resolutions, leading to each spot having multiple heterogeneous cells. Additionally, current spatial deconvolution methods lack the ability to utilize multi-modality information such as gene expression and chromatin accessibility from single-cell multi-omics data. In this study, we introduce a graph Contrastive Learning and Partial Least Squares regression-based method, CLPLS, to deconvolute ST data. CLPLS is a flexible method that it can be extended to integrate ST data and single-cell multi-omics data, enabling the exploration of the spatially epigenomic heterogeneity. We applied CLPLS to both simulated and real datasets coming from different platforms. Benchmark analyses with other methods on these datasets show the superior performance of CLPLS in deconvoluting spots in single cell level.
From eschatology to scatology: Recent work on Virgil’s Fourth Eclogue
Authors: Hejduk Julia D
Published: January 2025

This article provides an overview of scholarly work on Virgil’s Fourth Eclogue since the publication of Robin Nisbet’s ‘Virgil’s Fourth Eclogue: Easterners and Westerners’ (1978). It shows that, if anything, the mysteries and controversies surrounding Virgil’s mantic masterpiece have only deepened in recent decades.
Skin cancer risk in over 200.000 patients with haematologic malignancies in 30 years; a nationwide population-based study in the Netherlands
Authors: Eggermont Celeste J , Hollatz Andrya , Wakkee Marlies , Louwman Marieke , Dinmohamed Avinash G , Posthuma Eduardus F M , Nijsten Tamar , Hollestein Loes
Published: January 2025

Background

Patients with haematologic malignancies are at increased risk of developing skin cancer and often experience worse skin cancer-related outcomes. However, there is a lack of nationwide, population-based data with long-term follow-up on the incidence and risks of different skin cancer types across all haematologic malignancies.

Objectives

To assess population-based risk estimates for cutaneous squamous cell carcinoma (CSCC), malignant melanoma (MM), Merkel cell carcinoma (MCC), and basal cell carcinoma (BCC) among patients with haematologic malignancies, stratified by skin cancer type and haematologic malignancy subgroup. These estimates can serve as a base for surveillance guidelines and patient education.

Methods

This nationwide population-based epidemiologic cohort study used data on 210,794 patients diagnosed with a haematologic malignancy between 1989 and 2020 from the Netherlands Cancer Registry (NCR). In addition, data on each type of histopathologically confirmed skin cancer per patient after haematologic malignancy diagnosis was retrieved from the NCR. Patients with a history of skin cancer prior to their haematologic malignancy were excluded. Cumulative incidences, standardized incidence ratio’s (SIRs), and absolute excess risks for each of the four skin cancers were calculated and stratified by haematologic malignancy subgroup, age, sex, follow-up, and primary treatment.

Results

The overall 10-year cumulative incidence of developing a first skin cancer was 2.6% for CSCC, 0.5% for MM, 0.05% for MCC, and 4.8% for BCC. Compared to the general population, nearly all haematologic malignancy subgroups showed more than a twofold increased risk of CSCC, MM, MCC and BCC. Patients with chronic lymphocytic leukemia (CLL) showed the highest risks for each of the four skin cancers, with SIRs of 4.4 for CSCC, 2.7 for MM, 9.3 for MCC, and 2.6 for BCC. These elevated risks persisted for more than 30 years after haematologic malignancy diagnosis.

Conclusions

Patients with all types of haematologic malignancies, and especially those with CLL, have a lifetime increased risk of developing different types of skin cancer. These findings highlight the importance of creating awareness among patients and care providers about this increased risk and promoting sun-protective measures and regular skin self-examinations in this high-risk population.
Dynamic contrast enhanced MRI in nodal lymphoma: correlation of quantitative MR perfusion parameters with lymphoma subtype, Lugano stage, and Ki-67 index
Authors: Kataria Rohit , Ghasi Rohini Gupta , Kataria Satya Pal , Kolte Sachin
Published: January 2025

Background

Research into the intratumoural microenvironment in lymphoma has been escalated along with improved survival and new targeted therapies with an intent to refine risk stratification and prognostication. Various studies have reported significance of quantitative DCE-MRI parameters for predicting biological behaviour of various tumours. This study is an endeavour to supplement the existing literature on quantitative DCE-MRI in nodal lymphoma.

Objectives

To study the correlation of quantitative DCE-MRI parameters of Ktrans, Kep, and Ve with subtype, Lugano stage at diagnosis and Ki-67 proliferation index (PI) in nodal lymphoma.

Methods

33 patients of age >12 years with newly diagnosed nodal lymphoma underwent DCE-MRI. Ktrans, Kep, and Ve were generated from extended Tofts model and correlated with lymphoma subtype, Lugano staging, and Ki-67 PI.

Results

Mean Ktrans and Kep values were significantly higher in non-Hodgkin’s lymphoma than in Hodgkin’s lymphoma. Considering Ki-67 PI value of >45% as aggressive lymphoma, the mean Ktrans (659.37 × 10−3 min−1 vs 288.00 × 10−3 min−1, P < .001) and Kep (1256.63 × 10−3 min−1 vs 689.82 × 10−3 min−1, P = .004) values in aggressive lymphomas were significantly higher compared to non-aggressive lymphomas. ROC curve analysis revealed a threshold Ktrans value of ≥359 × 10−3 min−1 and Kep value of ≥853 × 10−3  min−1 for diagnosing aggressive lymphomas with a sensitivity of 95%, 90%, specificity of 100%,82%, and diagnostic accuracy of 91.7%,86.7%, respectively. There was no significant difference in DCE-MRI parameters of various Lugano stage subgroups.

Conclusion

DCE-MRI parameters have the potential to non-invasively predict the subtype, aggression and Ki-67 PI in nodal lymphoma.

Advances in knowledge

The knowledge that Ktrans is higher in aggressive lymphomas is novel. It adds to previous literature regarding MR perfusion in various neoplasms.
Short-term outcomes from the ‘Watch and Wait’ (WoW) study: prospective cohort study
Authors: Rydbeck Daniel , Azhar Najia , Blomqvist Lennart , Chabok Abbas , Folkesson Joakim , Gerdin Anders , Hermus Linda , Matthiessen Peter , Martling Anna , Nilsson Per J , Angenete Eva
Published: January 2025

Background

Despite absence of level 1 evidence on the long-term oncological safety of non-operative management for rectal cancer (watch and wait), increased implementation has occurred globally over the past decades. In Sweden, a pan-national prospective non-randomized study was initiated in 2017 to assess its implementation.

Method

Patients with biopsy-proven rectal cancer receiving neoadjuvant therapy according to national guidelines in whom a clinical complete response was detected at reassessment were eligible for inclusion following informed consent. Only patients with an opportunistic watch-and-wait approach were included. Inclusion and follow-up, according to the study protocol, was managed at the participating study centres. The primary outcome measure of the study is 3-year disease-free survival. Here, the secondary short-term outcomes local regrowth rate, distant metastasis rate and outcomes after surgery for regrowth, at 6 months follow-up, are reported.

Results

Between January 2017 and February 2023, 211 patients with a clinical complete response were included in the study. Thirty-three (16%) patients developed suspicious regrowth within 6 months of inclusion. Thirty-two of 33 patients had abdominal resectional surgery for regrowth. The curative intention rate was 94% for patients with regrowth. Three patients (1.4%) developed distant metastases within 6 months of inclusion.

Conclusion

This Swedish national study on watch and wait reports regrowth rates after 6 months are in line with previous reports in the literature. Nearly all patients with early regrowth could be treated with salvage surgery and curative intent.
The elusive relationship between retinal anatomy and brain amyloid
Authors: Grewal Dilraj S , Fekrat Sharon
Published: January 2025

This scientific commentary refers to ‘Retinal microstructure and microvasculature in association with brain amyloid burden’, by Egle et al. (https://doi.org/10.1093/braincomms/fcaf013).
Population concentration in high-complexity regions within city during the heat wave
Authors: Choi Hyoji , Kim Jonghyun , Yu Donghyeon , Jun Bogang
Published: January 2025

This study investigates the impact of the 2018 summer heat wave on urban mobility in Seoul and the role of economic complexity in the region’s resilience. Analysis of subway and mobile phone data reveals a significant decrease in the floating population during the extreme heat wave, underscoring the thermal vulnerability of urban areas. However, urban regions with higher complexity demonstrate resilience, attracting more visitors despite high temperatures. Our results suggest the centrality of economic complexity in urban resilience against climate-induced stressors. Additionally, high-complexity small business clusters appear to serve as focal points for sustaining urban vitality in the face of thermal shocks within the city. From a long-term perspective, our results imply that people might become more concentrated in highly complex regions in the era of global warming.
The Natural History of Inflammatory Bowel Disease in Adults With Common Variable Immunodeficiency: A Case Series From a Single US Tertiary Care Center
Authors: Jha Pankhuri , Elangovan Abbinaya , Chavan Akash Keluth , Cooper Gregory , Katz Jeffry , Cominelli Fabio , Regueiro Miguel , Mansoor Emad
Published: January 2025

Background

Common variable immunodeficiency (CVID) predisposes patients to inflammatory bowel disease (IBD). There are limited studies characterizing adults with concomitant CVID and IBD (CVID–IBD).

Methods

Demographics, clinical courses, endoscopic findings, and disease-specific therapies were obtained in adults ≥18 years with CVID–IBD over a 5-year period.

Results

We identified 11 patients with CVID–IBD, 6 with Crohn’s disease (CD), and 5 with ulcerative colitis (UC). The presenting symptoms in 10 (91%) were abdominal pain and diarrhea. A majority of patients were diagnosed with IBD before CVID. Patients with CVID–IBD were diagnosed with CVID at an older age compared to patients with CVID only. The most prevalent endoscopic finding in CD was either erythema or erosions in the ileum, whereas in UC, it was pancolitis. One patient with CD and 1 with UC required treatment with immunomodulators to achieve remission. Three patients with CD and 2 with UC required treatment with biologics to achieve remission. Eight received intravenous immunoglobulin (IVIG) for CVID. Four patients with CD and 1 with UC were diagnosed with either leukemia or lymphoma, and the most common malignancy was chronic lymphocytic leukemia (n = 3).

Conclusions

This is one of few studies evaluating demographic, clinical, endoscopic, histologic features, and therapeutic management in patients with CVID–IBD. Further studies are required to elucidate long-term differences in the clinical course and treatment of patients with CVID–IBD.
Testing the Waters: Exploring Why Democracies Have More Maritime Conflict
Authors: LaSpisa Chase , Mitchell Sara McLaughlin
Published: January 2025

While the democratic peace literature finds that pairs of democracies face lower risks for interstate conflict than other regime pairings, the maritime conflict literature often finds that democratic dyads have the highest risks for maritime diplomatic conflicts out of all regime pairings. Despite this surprising finding, there remains a gap for understanding what specific political mechanisms are driving democracies to engage in maritime conflict with other democracies. We explore whether democracies have more opportunities for maritime conflict generally, whether specific dimensions of democracy influence maritime conflict (domestic interests and executive constraints), including distinguishing between presidential and parliamentary democracies, and whether territorial integrity norms are weaker at sea. We find that coastal states are more democratic than landlocked states and that coastal dyads with maritime claims are more democratic than peaceful coastal dyads. We also show that multiple dimensions for democracy help explain the pattern of democratic maritime conflicts and that dyads with stronger domestic interests and more constrained executives (especially presidential democracies) are more likely to experience maritime conflicts. Finally, we show that territorial integrity norms have weaker effects on maritime conflict behavior, which helps us understand why democracies may be less constrained in their revisionist behavior in the maritime arena.
Massive Gene Loss in the Fungus Sporothrix epigloea Accompanied a Shift to Life in a Glucuronoxylomannan-based Gel Matrix
Authors: Allen Carmen C G , Díaz-Escandón David , DeLong-Duhon Sarah , Tagirdzhanova Gulnara , Huereca Alejandro , Reckseidler-Zenteno Shauna , Forbes Andrew , Spribille Toby
Published: January 2025

Fungi are well-known for their ability to both produce and catabolize complex carbohydrates to acquire carbon, often in the most extreme of environments. Glucuronoxylomannan (GXM)-based gel matrices are widely produced by fungi in nature and though they are of key interest in medicine and pharmaceuticals, their biodegradation is poorly understood. Though some organisms, including other fungi, are adapted to life in and on GXM-like matrices in nature, they are almost entirely unstudied, and it is unknown if they are involved in matrix degradation. Sporothrix epigloea is an ascomycete fungus that completes its life cycle entirely in the short-lived secreted polysaccharide matrix of a white jelly fungus, Tremella fuciformis. To gain insight into how S. epigloea adapted to life in this unusual microhabitat, we compared the predicted protein composition of S. epigloea to that of 21 other Sporothrix species. We found that the genome of S. epigloea is smaller than that of any other sampled Sporothrix, with widespread functional gene loss, including those coding for serine proteases and biotin synthesis. In addition, many predicted CAZymes degrading both plant and fungal cell wall components were lost while a lytic polysaccharide monooxygenase with no previously established activity or substrate specificity, appears to have been gained. Phenotype assays suggest narrow use of mannans and other oligosaccharides as carbon sources. Taken together, the results suggest a streamlined machinery, including potential carbon sourcing from GXM building blocks, facilitates the hyperspecialized ecology of S. epigloea in the GXM-like milieu.
The TRIM-NHL RNA-binding protein MEI-P26 modulates the size of Drosophila Type I neuroblast lineages
Authors: Hu Yichao , Yang Xiaohang , Lipshitz Howard D
Published: January 2025

The Drosophila TRIM-NHL RNA-binding protein (RBP), MEI-P26, has previously been shown to suppress tumor formation in the germline. Here we show that, in the Drosophila larval central brain, cell-type-specific expression of MEI-P26 plays a vital role in regulating neural development. MEI-P26 and another TRIM-NHL RBP, Brain tumor (BRAT), have distinct expression patterns in Type I neuroblast (NB) lineages: While both proteins are expressed in NBs, BRAT is expressed in ganglion mother cells (GMCs) but not neurons, whereas MEI-P26 is expressed in neurons but not GMCs. Knockdown of MEI-P26 leads to re-expression of the stem cell marker Deadpan (DPN) and over-production of neurons. In contrast, ectopically expressed MEI-P26 reduces NB lineage size by repressing division of GMCs, resulting in reduced neuron production. We show that MEI-P26 positively regulates expression of Prospero (PROS), a transcription factor that is known to repress cell cycle-related genes. Ectopic expression of PROS phenocopies ectopic expression of MEI-P26. In both cases, Cyclin B (CYCB) expression is downregulated. Importantly, knockdown of PROS in the context of ectopic MEI-P26 rescues the neural lineage. Based on these results, we conclude that MEI-P26 functions to prevent over-production of neurons by promoting production of PROS which, in turn, downregulates cell division.
International Conference – IP Protection for Plant Innovation 2024
Authors: Bosse Jocelyn
Published: January 2025

Plant intellectual property experts, key decision-makers, industry representatives, and professionals from around the world gathered in Amsterdam on 13 and 14 June 2024 for the 11th edition of the FORUM Institut’s biennial International Conference on IP Protection for Plant Innovation. The conference offered updates on the recent developments in plant intellectual property, as well as insights into the current debates in Europe and beyond. The talks provided international perspectives on a range of issues including plant-related patents; new genomic techniques; the new International Union for the Protection of New Varieties of Plants (UPOV) explanatory notes on essentially derived varieties; the regulation of digital sequence information; and the potential impact of the disclosure of origin requirement under the new World Intellectual Property Organisation (WIPO) Treaty on Intellectual Property, Genetic Resources and Associated Traditional Knowledge. This report provides a summary of the key points discussed at the conference. The next edition will take place in December 2026.
Mixed lipopeptide-based mucosal vaccine candidate induces cross-variant immunity and protects against SARS-CoV-2 infection in hamsters
Authors: Patel Raj S , Duque Diana , Bavananthasivam Jegarubee , Hewitt Melissa , Sandhu Jagdeep K , Kumar Rakesh , Tran Anh , Agrawal Babita
Published: January 2025

The global dissemination of SARS-CoV-2 led to a worldwide pandemic in March 2020. Even after the official downgrading of the COVID-19 pandemic, infection with SARS-CoV-2 variants continues. The rapid development and deployment of SARS-CoV-2 vaccines helped to mitigate the pandemic to a great extent. However, the current vaccines are suboptimal; they elicit incomplete and short-lived protection and are ineffective against evolving virus variants. Updating the spike antigen according to the prevailing variant and repeated boosters is not the long-term solution. We have designed a lipopeptide-based, mucosal, pan-coronavirus vaccine candidate, derived from highly conserved and/or functional regions of the SARS-CoV-2 spike, nucleocapsid, and membrane proteins. Our studies demonstrate that the designed lipopeptides (LPMix) induced both cellular and humoral (mucosal and systemic) immune responses upon intranasal immunization in mice. Furthermore, the antibodies bound to the wild-type and mutated S proteins of SARS-CoV-2 variants of concern, including Alpha, Beta, Delta and Omicron, and also led to efficient neutralization in a surrogate viral neutralization assay. Our sequence alignment and 3-dimensional molecular modeling studies demonstrated that spike-derived epitopes, P1 and P2, are sequentially and/or structurally conserved among the SARS-CoV-2 variants. The addition of a novel mucosal adjuvant, heat-killed Caulobacter crescentus, to the lipopeptide vaccine significantly bolstered mucosal antibody responses. Finally, the lipopeptide-based intranasal vaccine demonstrated significant improvement in lung pathologies in a hamster model of SARS-CoV-2 infection. These studies are fundamentally important and open new avenues in the investigation of an innovative, broadly protective intranasal vaccine platform for SARS-CoV-2 and its variants.
The Reachability Homology of a Directed Graph
Authors: Hepworth Richard , Roff Emily
Published: January 2025

The past decade has seen the development of path homology and magnitude homology—two homology theories of directed graphs, each satisfying classic properties such as Künneth and Mayer–Vietoris theorems. Recent work of Asao has shown that magnitude homology and path homology are related, appearing in different pages of a certain spectral sequence. Here we study the target of that spectral sequence, which we call reachability homology. We prove that it satisfies appropriate homotopy invariance, Künneth, excision, and Mayer–Vietoris theorems, these all being stronger than the corresponding properties for either magnitude or path homology.
Antibody-Based Antigen Delivery to Dendritic Cells as a Vaccination Strategy Against Ebola Virus Disease
Authors: Olal Catherine , Bodmer Bianca S , Rottstegge Monika , Escudero-Pérez Beatriz , Port Julia R , Bencsik András , Nelson Emily V , Heung Michelle , Wurr Stephanie , Blake Olivia , Adam Elisa , Oestereich Lisa , Baz-Martínez Maite , Müller-Guhl Jürgen , Gallais Yann , Anjuère Fabienne , Malliere Bernard , Idoyaga Juliana , Hoenen Thomas , Muñoz-Fontela César
Published: January 2025

Dendritic cells connect innate and adaptive immune responses. This is a particularly important immune checkpoint in the case of emerging infections against which most of the population does not have preexisting antibody immunity. In this study, we sought to test whether antibody-based delivery of Ebola virus (EBOV) antigens to dendritic cells could be used as a vaccination strategy against Ebola virus disease. Our approach was to use antibodies targeting the endocytic receptor DEC-205 present in murine and human dendritic cells, to deliver the EBOV nucleoprotein or the model antigen ovalbumin (OVA). Our findings indicate that DEC-205 targeting stimulated antigen-specific T-cell responses in mice, which resulted in protection from EBOV or recombinant EBOV-OVA challenge. An added value of this strategy was the generation of resident memory T cells. We propose that dendritic cell targeting could be used to improve T-cell responses against filoviruses, a strategy that may complement current vaccination strategies.
Associations Between the Gut Microbiome, Inflammation, and Cardiovascular Profiles in People With Human Immunodeficiency Virus
Authors: MacCann Rachel , Li Junhui , Leon Alejandro Abner Garcia , Negi Riya , Alalwan Dana , Tinago Willard , McGettrick Padraig , Cotter Aoife G , Landay Alan , Sabin Caroline , O’Toole Paul W , Mallon Patrick W G ,   for the Understanding the Pathology of Comorbid Disease in HIV-Infected Individuals (HIV UPBEAT) Study Group, McGettrick Padraig , Barco Elena Alvarez , Tinago Willard , Leon Alejandro Garcia , McDermott Aoife , McGinty Tara , Cotter Aoife G , Macken Alan , Mallon Patrick W G , Kavanagh Eoin , McCarthy Geraldine , Sheehan Gerard , Lambert John , Powderly William , Compston Juliet , Sabin Caroline
Published: January 2025

Background

Inflammation and innate immune activation are associated with chronic human immunodeficiency virus (HIV) infection, despite effective treatment. Although gut microbiota alterations are linked to systemic inflammation, their relationship with HIV infection the relationships between the gut microbiome, inflammation, and HIV remains unclear.

Methods

The HIV UPBEAT Coronary Artery Disease sub-study evaluated cardiovascular disease (CVD) in people with and without HIV. Subclinical CVD was assessed using coronary computed tomography angiography (CCTA). Thirty-four biomarkers were measured using quantitative immunoassays. Stool samples underwent 16S rRNA sequencing. Differentially abundant species were identified by analysis of compositions of microbiomes with bias correction (ANCOM-BC) and correlated to biomarkers, diet, and CCTA outcomes using Spearman correlation.

Results

Among 81 participants (median age, 51 years; 73% male), people with HIV (n = 44) had higher rates of hypercholesterolemia (P < .025). Gut microbiome β-diversity differed significantly by HIV status. Enriched Bifidobacterium pseudocatenulatum, Megamonas hypermegale, and Selenomonas ruminantium correlated with lower plaque burden, while depleted Ruminococcus bromii correlated with higher plaque burden and fat intake. Depleted Bacteroides spp and Alistepes spp correlated with elevated biomarkers (D-dimer, CD40 ligand, C-reactive protein, and interferon-γ).

Conclusions

Gut microbiota differences in people with HIV were linked to subclinical CVD, diet, and inflammation, highlighting the microbiome’s role in cardiovascular risk in HIV infection.
Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa
Authors: Liu Ya , Geng Yu , Jiang Yiru , Li Peng , Li Yue-zhong , Zhang Zheng
Published: January 2025

One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.
Tailoring generative AI chatbots for multiethnic communities in disaster preparedness communication: extending the CASA paradigm
Authors: Zhao Xinyan , Sun Yuan , Liu Wenlin , Wong Chau-Wai
Published: January 2025

This study is among the first to develop different prototypes of generative artificial intelligence (GenAI) chatbots powered by GPT-4 to communicate hurricane preparedness information to diverse residents. Drawing from the Computers Are Social Actors paradigm and the literature on disaster vulnerability and cultural tailoring, we conducted a between-subjects experiment with 441 Black, Hispanic, and Caucasian residents of Florida. Our results suggest that GenAI chatbots varying in tone formality and cultural tailoring significantly influence perceptions of their friendliness and credibility, which, in turn, relate to hurricane preparedness outcomes. These results highlight the potential of using GenAI chatbots to improve diverse communities’ disaster preparedness.
Laboratory and in-home evaluations of consumer- and professional-grade cockroach baits
Authors: Gordon Johnalyn M , Sierras Angela J , Jackson Daniela V , Principato Simona , DeVries Zachary C
Published: January 2025

German cockroaches (Blattella germanica (L.)) are a persistent pest in affordable housing and studies indicate that residents implement control on their own to deal with cockroaches within their homes. While many do-it-yourself (DIY) control options have proven ineffective, baits are widely considered to be a viable DIY solution for residents who do not have access to professional pest control services. To evaluate their efficacy, we tested consumer-use baits (Combat gel bait, Combat bait stations, and Hot Shot liquid bait stations) in both laboratory two-choice assays and in-home assays, comparing them with professional gel baits (Vendetta Nitro, Advion Evolution, and Maxforce FC Magnum). All baits (consumer- and professional-grade) caused > 80% mortality within 14 d in laboratory assays, including against home-collected German cockroach populations. However, the in-home efficacy of consumer-grade baits in comparison to their performance in laboratory assays was inconsistent, with some baits resulting in significant declines in trap catch in 1 month (Hot Shot liquid bait stations), some taking longer (Combat gel bait), and some never showing a decline (Combat bait stations). Discrepancies between product performance in laboratory and in-home studies are concerning and suggest that laboratory assays alone might not be indicative of the potential for control, especially in the context of the more complex home environment. Failures of consumer-grade baits may require re-evaluation of current recommendations for the use of consumer-grade cockroach baits as a viable control option for residents struggling with cockroach infestations without access to professional pest management.
Housing supply elasticity and government-owned land: evidence from Hong Kong
Authors: Ren Ren , Wong Siu Kei , Chau Kwong Wing
Published: January 2025

Housing supply elasticity is known to be related to three types of development constraints: topography, regulations, and scarcity of undeveloped land. This article shows that land ownership can also explain the spatial heterogeneity in supply elasticity if development costs differ between private and public land. Using data from Hong Kong (2003–2018), where government-owned land is common and has development advantages, this article confirms that the availability of government land contributes significantly to housing supply elasticity, in addition to the three constraints. This article sheds light on the potential of utilizing public land to increase housing supply.
Tumor localization strategies of multi-cancer early detection tests: a quantitative assessment
Authors: Tyson Christopher , Li Kevin H , Cao Xiting , O’Brien James M , Fishman Elliot K , O’Donnell Elizabeth K , Duran Carlos , Parthasarathy Vijay , Rego Seema P , Choudhry Omair A , Beer Tomasz M
Published: January 2025

Background

Multi-cancer early detection (MCED) tests may expand cancer screening. Characterizing diagnostic resolution approaches following positive MCED tests is critical. Two trials employed distinct resolution approaches: a molecular signal to predict tissue of origin (TOO) and an imaging-based diagnostic strategy. This modeling study characterizes diagnostic journeys and impact in a hypothetical population of average risk MCED eligible patients.

Methods

A mathematical expression for diagnostic burden was derived using positive predictive value (PPV), molecular TOO localization accuracy, and numbers of procedures associated with each diagnostic outcome. Imaging-based and molecular TOO-informed strategies were compared. Excess lifetime cancer risk due to futile radiation exposure was estimated using organ-specific diagnostic imaging radiation doses.

Results

Across all PPVs and localization performances, a molecular TOO strategy resulted in a higher diagnostic burden: 3.6 procedures [SD 0.445] vs 2.6 procedures [SD 0.100] for the imaging strategy. Estimated diagnostic burden was higher for molecular TOO in 95.5% of all PPV and TOO accuracy combinations; ≥79% PPV and 90% accuracy would be required for a molecular TOO-informed strategy to be less burdensome than imaging. The maximum rate of excess cancer incidence from radiation exposure for MCED false positive results (individuals aged 50-84) was 64.6/100,000 (annual testing, 99% specificity), 48.5/100,000 (biennial testing, 98.5% specificity), and 64.6/100,000 (biennial testing, 98% specificity).

Conclusions

An imaging-based diagnostic strategy is more efficient than a molecular TOO-informed approach across almost all PPV and TOO accuracy combinations. The use of an imaging-based approach for cancer localization can be efficient and low-risk compared to a molecular-informed approach.
The Legislative Adjustment of Chinese Enforcement Regulation of the International Commercial Settlement Agreement in the context of the Singapore mediation convention
Authors: Xiong Hailiang
Published: January 2025

The United Nations Convention on International Settlement Agreements Resulting from Mediation has established an external legal framework for the cross-border enforcement of international commercial mediation settlement agreements. By virtue of the two-aspect institutional design, this Convention has constructed a modern mechanism for the direct enforcement of international commercial mediated settlement agreements. As one of the first signatories, China does not yet have the specific mediation legislation to conform to the Convention and cannot channel the Singapore Convention. This article discussed the dilemma of the ratification of the Singapore Convention in China from a comparative perspective and argues that China should adjust its mediation regulation by reducing the requirement of application for enforcement and limiting the judicial supervision to establish a direct enforcement mechanism following the potential international obligation under the Singapore Convention and further refine the macro mediation system.
Tiaogan Jiejiu Tongluo formula alleviates hepatic steatosis in NAFLD mice by regulating AMPK signaling pathway
Authors: Lei Yuting , Wang Lianping , Song Linze , Han Jiajun , Ma He , Luo Haoming , Ma Yan , Han Dong
Published: January 2025

Objectives

Tiaogan Jiejiu Tongluo formula (TJTF) is a traditional Chinese medicine formula for liver disease. The purpose of this study was to explore the protective effects and mechanisms of TJTF on nonalcoholic fatty liver disease (NAFLD) mice.

Methods

A NAFLD model of mice was established by a combination of a high-fat diet and CCL4 and then treated with TJTF. The damage to liver tissue was observed through histopathology, and the levels of AST, ALT, TG, TC, LDL-C, and HDL-C in the serum, as well as SOD, GSH, and MDA in the liver tissue were determined using biochemistry or ELISA kit. The expression of proteins related to the AMPK pathway was detected by western blotting.

Results

Biochemical indicators and pathological examination showed that TJTF could enhance the antioxidant capacity of liver tissue and significantly reduce liver lipid deposition. In addition, TJTF significantly increased levels of LKB1 and p-AMPK, and decreased the levels of HMGCR, SREBP-1c, FAS, and ACC.

Conclusion

TJTF can alleviate hepatic steatosis and effectively improve NAFLD by regulating AMPK signaling pathway in NAFLD mice.
A review of the environmental spread of Salmonella enterica serovars through water in Africa
Authors: Rabiu Akeem Ganiyu , Fadiji Oyinkansola , Adesoji Ayodele Timilehin , Jimoh Simiat Olanike , Cho Sohyun
Published: January 2025

Salmonella is an enteric pathogenic bacterium in mammals that thrives in sewage, soil, and aquatic environments because of its wide ecological adaptability. The spread of Salmonella infection is associated with a lack of clean water, poor hygiene, and poor sanitation in developing countries. However, the input of Salmonella-contaminated surface water and groundwater in the environmental dissemination of antimicrobial-resistant Salmonella is obscure outside developed countries. This study aimed to assess literature that described Salmonella from groundwater, surface water, and treated water in Africa and profiled the bacteria for antimicrobial resistance (AMR). We seek to highlight the pitfalls in S. enterica identification schemes and determine the entry routes of S. enterica into surface water and groundwater to comprehend the spread patterns of S. enterica through the water ecosystem. Salmonella was frequently recovered not only from groundwater but also from unprotected springs and river water in Africa. However, the insufficiency of standard methods limited the speciation of the bacteria and only a few studies determined the isolates’ AMR patterns. Integrating the Salmonella surveillance in environmental and treated water into the global Salmonella surveillance can assist in controlling typhoid fever spread and generally reduce the burden of waterborne infections in Africa.
Conformans novas selves: The significance of Balkan route migrants’ possible and future narrative identities
Authors: Poppi Fabio Indìo Massimo
Published: January 2025

This study explores the multifaceted nature of narrative identities among migrants, emphasizing the importance of possible and future dimensions. Drawing on interviews with fifteen men from Pakistan, Afghanistan, Iraq, Syria, and Bangladesh who traveled the Balkan route to Trieste (Italy), the research examines how temporal influences, narrative disruptions, reverse cultural enrichment, and the significance of revenge shape their identities. Integrating biographical and interactional approaches, the study highlights how migrants use narratives to bridge past experiences with future aspirations, creating coherence in their personal histories. These narrative identities provide psychological resilience, meaning-making, and empowerment, allowing migrants to envision and actively shape their futures. By addressing the underexplored potential and future aspects of narrative identity, this research contributes to a more comprehensive understanding of identity construction in the context of migration, offering insights into the dynamic and transformative power of narratives in shaping personal and social realities.
Impact of an institutional antifungal stewardship program on antifungal usage and outcomes in patients with invasive fungal infections
Authors: Sachdev Janya , Gourav Sudesh , Xess Immaculata , Soneja Manish , Punjadath Sryla , Siddharth Vijaydeep , Pandey Mragnayani , Gupta Sonakshi , Manhas Aish , Rana Bhaskar , Appasami Kavi Priya , Singh Gagandeep
Published: January 2025

Therapeutic and prophylactic use of antifungals is rising continuously. However, inadequate awareness of diagnostic and treatment guidelines and limited laboratory modalities lead to inappropriate use. This study assessed the impact of an institutional antifungal stewardship program on antifungal use practices and patient outcomes. In the pre-intervention phase, data was collected regarding antifungal therapy among patients with invasive fungal infections. Appropriateness of antifungal prescription was assessed. In the intervention phase, simple algorithms for diagnosis and management of fungal infections were prepared from international guidelines and incorporated into a booklet for distribution. Monthly training sessions were conducted. New serological and molecular tests and therapeutic drug monitoring were introduced. In the post-intervention phase, an antifungal stewardship team was constituted for clinical advisory on demand and ongoing training. Data regarding antifungal therapy was collected and compared with pre-intervention data. Untreated patients decreased from 25% to 18.9% post-intervention (P = .28). Appropriate antifungal use increased from 72.6% to 77.9% (P = .4) among patients with a single fungal infection, and from 57.1% to 88.5% (P = .04) for at least one infection among those with dual fungal infections. 49 incidents of inappropriate use in various categories were seen among 75 patients receiving antifungals pre-intervention, decreasing to 42 incidents among 94 patients post-intervention (P = .06), particularly evident among patients with dual infections (P = .002). Mortality increased from 51% to 75.86% post-intervention (P = .0001). Overall, the small improvement noticed in antifungal usage pattern can still be considered significant, given the limited study period.
Evidence for magneto-gravitational processes in supermassive black hole binary PG 1553+113
Authors: Zhang Haiyun , Yan Dahai , Zhang Li , Tang Niansheng
Published: January 2025

PG 1553+113 has drawn significant attention for its quasi-periodic oscillation (QPO) in $\gamma$-ray variability, though the origin of its variability remains uncertain. In this study, we propose a physical mechanism to explain the observed $\gamma$-ray variability within the framework of a supermassive black hole binary (SMBHB) system, supported by a newly identified component hidden in the light curve. A detailed analysis for its $\sim$16-yr light curve obtained from Fermi-LAT observations is performed by Gaussian process. As anticipated, the QPO of 2.1 yr ($771\pm 8$ d) is effectively captured by the stochastically driven damped simple harmonic oscillator kernel within the underdamped regime, and the overall stochastic nature of the variability is described by the damped random walk (DRW) kernel albeit with an unconstrained damping time-scale. Additionally, our results reveal a previously unrecognized component in active galactic nuclei variability, characterized by the Mat$\acute{\rm e}$rn$-3/2$ kernel, which is typically associated with systems undergoing abrupt energy release. These findings can be consistently interpreted within the SMBHB framework. The QPO of $\sim$2.1 yr is likely attributed to the orbital motion in a SMBHB system. The Mat$\acute{\rm e}$rn$-3/2$ component is interpreted as resulting from magnetic reconnection events triggered by gravitational perturbations of the magnetic field within the jet, occurring as one black hole approaches the other. Meanwhile, in this case, the damping time-scale of the common DRW kernel remains unconstrained due to the influence of new perturbations within the system.
The nature and evolution of early massive quenched galaxies in the simba-C simulation
Authors: Szpila Jakub , Davé Romeel , Rennehan Douglas , Cui Weiguang , Hough Renier T
Published: January 2025

We examine the nature, origin, and fate of early ($z\ge 2$) massive ($M_\star \gt 10^{10}\,\mathrm{ M}_\odot$) quenched galaxies (EQGs) in a new $(100\,h^{-1}\,{\rm Mpc}^3)$ run of the simba-C galaxy formation model. We define ‘quenched’ to be $\gt 4\sigma$ below an iterative polynomial fit to the star-forming sequence (SFS), and find that simba-C produces EQGs as early as $z\sim 5$ and number densities agreeing with observations at $z\lesssim 3$ (though slightly low at $z\gtrsim 4$). Using a photometric-based EQG selection or a fixed specific star formation rate cut of $10^{-10}$ yr$^{-1}$ yields similar results. EQGs predominantly arise in central galaxies with stellar mass $M_\star \sim 10^{10.5-11.3}\,\rm{M}_\odot$, not necessarily the most massive systems. A Uniform Manifold Approximation and Projection shows that quenched galaxies have notably large black hole-to-stellar mass ratios, lower rotational support, and less dust, but are not atypical versus similar-mass non-EQGs in their environments, halo mass, or halo gas temperatures at the time of quenching. However, via galaxy tracking we show that the progenitor environments of EQGs are significantly more overdense than that of non-EQGs, which drives higher black hole mass fractions and stellar-to-halo mass ratios. This results in the Eddington ratio dropping sufficiently low for simba-C’s jet mode feedback to turn on, which quickly quenches the host galaxies. EQGs thus seem to be galaxies that grow their black holes quickly within highly dense environments, but end up in moderately dense environments where black hole feedback can quench effectively. We find that $\gtrsim 30~{{\ \rm per\ cent}}$ of EQGs rejuvenate, but the rejuvenating fraction drops quickly below $z\lesssim 2$. By $z=0$, it is difficult to distinguish the descendants of EQGs versus non-EQGs.
Comprehensive analysis of four Kepler eclipsing binaries possessing solar-type components on wide eccentric orbits
Authors: Özdarcan Orkun , Çakırlı Ömür
Published: January 2025

Such spectroscopic and photometric studies have opened up a window into the interiors of solar-type stars that are found in eclipsing binaries, which is proving to be a remarkable facility of knowledge to test models of stellar evolution. Until recently, numerous cases had been analysed using Kepler data. To further clarify this research, we investigate four long-period detached eclipsing binaries: KIC 8868907, KIC 8610483, KIC 9948002, and KIC 11769146. Our findings revealed that the target systems are composed of solar-type components in a wide and very eccentric orbit. Simultaneous orbital and light-curve solutions indicate that the computed stellar radii and masses of the components of KIC 8868907, KIC 9948002, and KIC 11769146 align with theoretical models within the uncertainties. We observe a curious case for KIC 8610483 whose components are very likely main-sequence stars and possess lower mass than our Sun but are positioned very close to the terminal age main sequence due to their significantly large radii compared to a classical main-sequence star with a similar mass. Predictions of circularization theories suggest that none of the target systems will reach a circular orbit before the end of their main-sequence phases.