bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of RNA interference and pattern‐triggered immunity induced by dsRNA reveals different efficiencies in the antiviral response to potato virus X
Authors: Necira Khouloud , Contreras Lorenzo , Kamargiakis Efstratios , Kamoun Mohamed Selim , Canto Tomás , Tenllado Francisco 
Published: September 2024

AbstractAntiviral responses induced by double‐stranded RNA (dsRNA) include RNA interference (RNAi) and pattern‐triggered immunity (PTI), but their relative contributions to antiviral defence are not well understood. We aimed at testing the impact of exogenous applied dsRNA on both layers of defence against potato virus X expressing GFP (PVX‐GFP) in Nicotiana benthamiana. Co‐inoculation of PVX‐GFP with either sequence‐specific (RNAi) or nonspecific dsRNA (PTI) showed that nonspecific dsRNA reduced virus accumulation in both inoculated and systemic leaves. However, nonspecific dsRNA was a poor inducer of antiviral immunity compared to a sequence‐specific dsRNA capable of triggering the RNAi response, and plants became susceptible to systemic infection. Studies with a PVX mutant unable to move from cell to cell indicated that the interference with PVX‐GFP triggered by nonspecific dsRNA operated at the single‐cell level. Next, we performed RNA‐seq analysis to examine similarities and differences in the transcriptome triggered by dsRNA alone or in combination with viruses harbouring sequences targeted or not by dsRNA. Enrichment analysis showed an over‐representation of plant‐pathogen signalling pathways, such as calcium, ethylene and MAPK signalling, which are typical of antimicrobial PTI. Moreover, the transcriptomic response to the virus targeted by dsRNA had a greater impact on defence than the non‐targeted virus, highlighting qualitative differences between sequence‐specific RNAi and nonspecific PTI responses. Together, these results further our understanding of plant antiviral defence, particularly the contribution of nonspecific dsRNA‐mediated PTI. We envisage that both sequence‐specific RNAi and nonspecific PTI pathways may be triggered via topical application of dsRNA, contributing cumulatively to plant protection against viruses.
Diagnostic Accuracy of Dermatoscopy Versus Microbiological Culture and Polymerase Chain Reaction in the Diagnosis of Onychomycosis: A Cross‐Sectional Study
Authors: Navarro‐Pérez David , Tardáguila‐García Aroa , García‐Oreja Sara , León‐Herce Diego , Álvaro‐Afonso Francisco Javier , Lázaro‐Martínez José Luis 
Published: September 2024

ABSTRACTBackgroundSeveral clinical signs in dermatoscopy are very characteristic of onychomycosis and can be a quick complement for the diagnosis of onychomycosis.ObjectivesThe aim of this study was to evaluate the diagnostic accuracy of dermatoscopy compared to microbiological culture and polymerase chain reaction (PCR), as well as the clinical signs associated with onychomycosis.MethodsThe clinical signs of 125 patients were assessed cross‐sectionally using dermatoscopy, and a positive or negative result was assigned. A sample was then taken for PCR and microbiological culture.ResultsOf the 125 patients, 69.6% (87/125) had positive results when both laboratory tests were combined. When they were not combined, the prevalence was lower at 48% (60/125) with PCR and at 43.2% (54/125) with culture. Furthermore, 76.8% (96/125) were classified as positive with dermatoscopy with a sensitivity of 1, a specificity of 0.76, positive predictive value of 0.91 and negative predictive value of 1 (with 95% confidence intervals). Of the 96 dermatoscopy‐positive samples, 36 were negative with PCR (p < 0.001), 42 were negative with culture (p < 0.001) and nine were negative when both tests were combined (p < 0.001). Clinical signs that were significantly associated with the presence of onychomycosis were subungual hyperkeratosis (dermatoscopy: p = 0.004, odds ratio (OR) = 2.438; PCR + microbiological culture: p = 0.004, OR = 3.221), subungual detritus (p = 0.033, OR = 3.01, only with dermatoscopy) and dermatophytoma (dermatoscopy: p = 0.049, OR = 3.02; PCR + microbiological culture: p = 0.022, OR = 2.40).ConclusionsThe results suggest that dermatoscopy is a good tool for the diagnosis of onychomycosis but should be used as a complementary test or for screening patients to be sampled for laboratory testing. The combination of the three tests can lead to a reduction of false‐positive and false‐negative clinical and laboratory results. This allows for early diagnosis and specific treatment based on test results.
Crafting a national identity: The role of geography textbooks in 1930s Turkey's nation‐building project
Authors: Gür Hande , Çalışkan Gül 
Published: September 2024

AbstractThis paper investigates geography textbooks of the 1930s in Turkey, contending that geographical knowledge played a pivotal role in shaping nationhood within a modernising state. This study's critical discourse analysis (CDA) of the early republican geography textbooks showcases how (1) Turkey's spatial formation was reimagined in 1930s; (2) defining markers of Turkishness and the Turkish nation were forged through erasures and breakups of minority groups, and (3) the new national identity was “bridged” to the geography of the newly founded Republic. This paper posits that a nation's portrayal of its geography and global positioning is not merely a factual recording, but also a reflection of ideological and political choices. Such portrayals are complete social constructs, inherently influenced by power dynamics and disputes. Beneath the ostensibly impartial depictions of space and spatial relations, invisible power dynamics and assertions underlie the assignments of specific meanings to geographic areas.
Sepsis‐associated acute kidney injury in patients with chronic kidney disease: Patient characteristics, prevalence, timing, trajectory, treatment and associated outcomes
Authors: White Kyle C. , Bellomo Rinaldo , Tabah Alexis , Attokaran Antony G. , White Hayden , McCullough James , Shekar Kiran , Ramanan Mahesh , Garrett Peter , McIlroy Philippa , Senthuran Siva , Luke Stephen , Serpa‐Neto Ary , Larsen Tom , Laupland Kevin B. ,   the Queensland Critical Care Research Network (QCCRN)
Published: September 2024

AbstractAimThe features and outcomes of sepsis‐associated acute kidney injury (SA‐AKI) may be affected by chronic kidney disease (CKD). Accordingly, we aimed to compare SA‐AKI in patients with or without CKD.MethodsRetrospective cohort study in 12 intensive care units (ICU). We studied the prevalence, patient characteristics, timing, trajectory, treatment and outcomes of SA‐AKI with and without CKD.ResultsOf 84 240 admissions, 7255 (8.6%) involved patients with CKD. SA‐AKI was more common in patients with CKD (21% vs 14%; p < .001). CKD patients were older (70 vs. 60 years; p < .001), had a higher median Charlson co‐morbidity index (5 vs. 3; p < .001) and acute physiology and chronic health evaluation (APACHE) III score (78 vs. 60; p < .001) and were more likely to receive renal replacement therapy (RRT) (25% vs. 17%; p < .001). They had less complete return to baseline function at ICU discharge (48% vs. 60%; p < .001), higher major adverse kidney events at day 30 (MAKE‐30) (38% vs. 27%; p < .001), and higher hospital and 90‐day mortality (21% vs. 13%; p < .001, and 27% vs. 16%; p < .001, respectively). After adjustment for patient characteristics and severity of illness, however, CKD was not an independent risk factor for increased 90‐day mortality (OR 0.88; 95% CI 0.76–1.02; p = .08) or MAKE‐30 (OR 0.98; 95% CI 0.80–1.09; p = .4).ConclusionSA‐AKI is more common in patients with CKD. Such patients are older, more co‐morbid, have higher disease severity, receive different ICU therapies and have different trajectories of renal recovery and greater unadjusted mortality. However, after adjustment day‐90 mortality and MAKE‐30 risk were not increased by CKD.
Differential expression of vitellogenin in the brain of Solenopsis invicta workers based on social and nutritional context
Authors: Hawkings Chloe , Tamborindeguy Cecilia 
Published: September 2024

AbstractVitellogenin (Vg) has been recognized as a co‐opted gene involved in social colonies where it is associated with reproduction in the queen and task transitions in workers. The Solenopsis invicta genome harbours four Vg genes, Vg1, Vg2, Vg3 and Vg4, and this study explored the regional expression of these genes in the brain and head of the worker caste in different subcaste and social contexts. Transcriptomic analyses of the worker brain while in the presence or absence of brood revealed differential expression of genes involved with social behaviours. Among these, we found higher expression of Vg2 and Vg3 in the brains of workers in the absence of brood. The influence of brood on expression of Vg between worker castes was also investigated. RT‐qPCR revealed higher expression of Vg in the head of workers in the absence of brood. Further studies demonstrated that Vg was also differentially expressed in the heads of workers conducting specific tasks and differing between subcastes. Nurses maintained higher Vg expression than foragers. We conclude worker Vg expression may be linked to the brood and/or nutritional state. Vg expression changes when workers are deprived of protein suggesting it is regulated by nutritional signalling and the presence of brood.
Meloidogyne hapla dominates plant‐parasitic nematode communities associated with kiwifruit orchards in Portugal
Authors: Gonçalves A. Rita , Conceição I. Luci , Carvalho Rui P. , Costa Sofia R. 
Published: September 2024

AbstractKiwifruit, Actinidia spp., is an important crop worldwide and its cultivation has been increasing in Portugal. Kiwifruit plants are susceptible to plant‐parasitic nematodes (PPNs), including Meloidogyne spp. M. hapla and M. incognita have been reported to affect kiwifruit in major production regions worldwide, although information is lacking on the distribution and identity of PPNs associated with kiwifruit orchards in Portugal. Moreover, research is scarce on the drivers of PPN communities in this crop. Our primary objective was to investigate the diversity, density and distribution of PPNs within kiwifruit orchards of Portugal and to elucidate the influence of environmental factors on their community composition. Additionally, we aimed to evaluate population densities and identity of Meloidogyne spp. Nematodes were extracted from composite soil and root samples collected from orchards. Analysis of soil nematode communities suggested bacterial‐driven decomposition and high nutrient enrichment in these soils. Sixteen different genera of PPNs were detected, with Meloidogyne spp. as the dominant genus, mostly represented by a single species, M. hapla. PPN communities exhibited low richness, and β‐diversity analysis indicated a high degree of similarity among them. Additionally, their composition was significantly influenced by soil and climatic parameters. We found that 37 out of 40 kiwifruit orchards in Portugal were infested by root‐knot nematodes. The unexpectedly low species diversity, dominated by M. hapla, merits further research to establish underlying factors for its high incidence in this crop and to assess the impact of these nematodes on kiwifruit performance and productivity.
ScRNA‐seq reveals the spatiotemporal distribution of camptothecin pathway and transposon activity in Camptotheca acuminata shoot apexes and leaves
Authors: Wang Shu , Zhang Chuyi , Li Ying , Li Rucan , Du Ke , Sun Chao , Shen Xiaofeng , Guo Baolin 
Published: September 2024

AbstractCamptotheca acuminata Decne., a significant natural source of the anticancer drug camptothecin (CPT), synthesizes CPT through the monoterpene indole alkaloid (MIA) pathway. In this study, we used single‐cell RNA sequencing (scRNA‐seq) to generate datasets encompassing over 60,000 cells from C. acuminata shoot apexes and leaves. After cell clustering and annotation, we identified five major cell types in shoot apexes and four in leaves. Analysis of MIA pathway gene expression revealed that most of them exhibited heightened expression in proliferating cells (PCs) and vascular cells (VCs). In contrast to MIA biosynthesis in Catharanthus roseus, CPT biosynthesis in C. acuminata did not exhibit multicellular compartmentalization. Some putative genes encoding enzymes and transcription factors (TFs) related to the biosynthesis of CPT and its derivatives were identified through co‐expression analysis. These include 19 cytochrome P450 genes, 8 O‐methyltransferase (OMT) genes, and 62 TFs. Additionally, these pathway genes exhibited dynamic expression patterns during VC and EC development. Furthermore, by integrating gene and transposable element (TE) expression data, we constructed novel single‐cell transcriptome atlases for C. acuminata. This approach significantly facilitated the identification of rare cell types, including peripheral zone cells (PZs). Some TE families displayed cell type specific, tissue specific, or developmental stage‐specific expression patterns, suggesting crucial roles for these TEs in cell differentiation and development. Overall, this study not only provides novel insights into CPT biosynthesis and spatial–temporal TE expression characteristics in C. acuminata, but also serves as a valuable resource for further comprehensive investigations into the development and physiology of this species.
Number of Blastodisc Cells During the Laying Period for Two Successive Generations of Layer and Broiler Breeder
Authors: Bernardi Ophélie , Fréville Mathias , Ramé Christelle , Reverchon Maxime , Dupont Joëlle 
Published: September 2024

ABSTRACTIn the poultry industry, genetic selection for growth performance is associated with poor reproductive efficiency and an increase in embryo mortality. The identification of new biomarkers is essential to improve these parameters. The blastodisc, composed of blastodermal cells, undergoes cellular events to achieve embryo development. Factors such as hen's age, temperature and time of egg storage could influence the number of blastodermal cells and impair embryo development. In this study, we investigated the variability of the number of viable cells of blastodisc (NVCB) that could be dependent on the stage of laying and on the breed and potentially associated with reproductive parameters. In experimental breeds, eggs were collected during the whole cycle of laying. Then, the protocol was repeated on industrial breeds (breeder hens) during five successive days at three stages of laying (before, after laying peak and at the end of laying period) for two generations (mothers and offsprings). For each egg, the blastodisc was dissected in order to count viable cells. For both experiments, the NVCB increased during the laying cycle. The NVCB was higher in broiler blastodisc compared to layer blastodisc for both generations. For layer breed, the NVCB were negatively correlated with laying rate for the first generation while positively associated for offsprings. However, the NVCB was positively correlated with laying rates in both generations for broiler hens and with fertility and hatchability rates. The NVCB from fresh oviposited fertilised eggs could be a potential tool in predicting on reproductive performances in poultry.
Epistemic attunements: Experiments in intermedial anthropology
Authors: Deger Jennifer , Coffey Victoria Baskin , Kingston Caleb , Lowe Sebastian J. , Stefanoff Lisa 
Published: September 2024

Abstract‘Epistemic attunements – Regenerating anthroplogy's form’ is a collective experiment in expanding the expressive and analytic repertoire of anthropology and related disciplines. It features eleven peer‐reviewed research articles published on a standalone website that has been designed, built, and maintained by our editorial collective, independent of Wiley's infrastructure and oversight. The result is a unique off‐grid adventure in academic publishing that seeks to contribute to the re‐orientation and outward opening of a discipline long committed to finding new ways to apprehend—and respond to—worlds undergoing constant, messy, and often‐brutal transformation. In this essay we describe the making of this double special issue of TAJA to make the case for intermedial research and co‐design as regenerative praxis.
Improvisations towards a sonorous ethics in Aotearoa New Zealand
Authors: Lowe Sebastian J. 
Published: September 2024

AbstractTaonga puoro is a Māori instrumental tradition through which one cultivates an improvisational form of playing with the world. It does not follow musical notation. ‘Instruments’ vary from rocks, to bones, wood and other non‐traditional materials, such as glass. They can be found in situ, or carefully crafted and gifted. Each performance is different, new and responsive not only to the riffing soundings of fellow humans but also to the wider worlds of more‐than‐human sensuous agency with which we attune, respond and participate. In both their materiality and their performativity, taonga puoro draws attention to points of convergence, in which histories, ancestors, human and more‐than‐human entities mingle as affective co‐collaborators in a world already playing in co‐composition. Thinking and riffing with this idea of co‐composition as a practice of attuning to how I participate in the world that I have come to know, this sound–image–text article is made to revisit and dwell within moments of creative‐critical world‐making through playing with my close friend Jessica Kahukura (Te Ātihaunui‐a‐Pāpārangi, Ngā Rauru, Ngāti Kahungunu, Ngāti Tūwharetoa). It focuses particularly on my own practices as a Pākehā (non‐Māori New Zealander) researcher‐musician by attuning to my creative‐critical positionality in relation to a broader politics and ethics of participation and invention.
Data-Driven Modeling of Tire–Soil Interaction With Proper Orthogonal Decomposition-Based Model Order Reduction
Authors: Okada Taiki , He Hao , Yamashita Hiroki , Sugiyama Hiroyuki 
Published: September 2024

Abstract
A data-driven model capable of predicting time-domain solutions of a high-fidelity tire–soil interaction model is developed to enable quick prediction of mobility capabilities on deformable terrain. The adaptive model order reduction based on the proper orthogonal decomposition (POD), for which the high-dimensional equations are projected onto the reduced subspace, is utilized as the basis for predicting the time-domain tire–soil interaction behavior. The projection-based model order reduction, however, requires many online matrix operations due to the successive updates of the nonlinear functions and Jacobians at every time-step, thereby hindering the computational improvement. Therefore, a data-driven approach using a long short-term memory (LSTM) neural network is introduced to predict the reduced order coordinates without the projection and time integration processes for computational speedup. With this model, a hybrid data-driven/physics-based off-road mobility model is proposed, where four separate LSTM-POD data-driven tire–soil interaction models are integrated into the physics-based multibody dynamics (MBD) vehicle model through a force–displacement coupling algorithm. By doing so, the individual data-driven tire–soil interaction model can be constructed efficiently, and the MBD and LSTM models are assembled as a single off-road mobility model and analyzed with existing off-road mobility solvers. The predictive ability and computational benefit of the proposed data-driven tire–soil interaction model with the POD-based model order reduction are examined with several numerical examples.
Heat resistance differences are common between both vegetative cells and spores of
Clostridium perfringens
type F isolates carrying a chromosomal vs plasmid-borne enterotoxin gene
Authors: Mehdizadeh Gohari Iman , Li Jihong , Shivers Robert , Sparks Shauna G. , McClane Bruce A. 
Published: September 2024

ABSTRACT

Clostridium perfringens
type F isolates utilize
C. perfringens
enterotoxin (CPE) to cause food poisoning (FP) and nonfoodborne gastrointestinal diseases. The enterotoxin gene (
cpe
) can be located on either the chromosome or plasmids, but most FP isolates carry a chromosomal
cpe
(c
-cpe
) gene. Our 2000 article in
Applied and Environmental Microbiology
(66:3234–3240, 2000,
https://doi.org/10.1128/aem.66.8.3234-3240.2000
https://doi.org/10.1128/AEM.66.8.3234-3240.2000
) determined that vegetative cells and spores of c-
cpe
isolates are more heat resistant than those of plasmid
cpe
(p-
cpe
) isolates, which is favorable for their survival in improperly cooked or held food. However, that 2000 article was recently retracted (90:e00249-24, 2024,
https://doi.org/10.1128/aem.00249-24
). To our knowledge, the 2000 article remains the only study reporting that heat resistance differences are common between both vegetative cells and spores of type F c-
cpe
isolates vs type F p-
cpe
isolates. To confirm and preserve this information in the literature, the heat resistance portion of the 2000 study has been repeated. The 2024 results reproduced the 2000 results by indicating that, relative to the surveyed type F p-
cpe
isolates, the vegetative cells of surveyed type F c-
cpe
isolates are ~2-fold more heat resistant and the spores of most surveyed c-
cpe
isolates are ~30-fold more heat resistant. However, consistent with several reports since our 2000 paper, one surveyed type F c-
cpe
isolate (which did not appreciably sporulate in 2000 but sporulated in 2024) produced spores with intermediate heat sensitivity, confirming that spores of some type F c-
cpe
isolates lack exceptional heat resistance.

IMPORTANCE

Clostridium perfringens
type F food poisoning (FP), which is the second most common bacterial cause of FP, involves the production of
C. perfringens
enterotoxin. While the enterotoxin gene (
cpe
) can be located on either the chromosome or plasmids in type F isolates, most FP cases are caused by chromosomal
cpe
isolates. The current results support the conclusion that the vegetative cells and spores of type F chromosomal
cpe
isolates are often more heat resistant than vegetative cells and spores of type F plasmid
cpe
isolates. Greater heat resistance should favor the survival of the spores and vegetative cells of those chromosomal
cpe
isolates in temperature-abused food, which may help explain the strong association of type F chromosomal
cpe
strains with FP.