bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic Testing Accuracy of Sucrose-stimulated Salivary pH for Screening Early Childhood Caries Diagnosis and Severity: An Observational Study
Authors: Okuji David , Tian Victoria , Odusanwo Olutayo , Twi-Yeboah Alberta 
Published: February 2025

ABSTRACTPurposeThe purpose of this study was to determine the diagnostic testing accuracy of child and maternal sucrose-stimulated salivary pH as screening tools for early childhood caries diagnosis and severity.MethodsFrom a sample population of 642 mother-child dyads, with child-subjects under age six years old, child and maternal sucrose-stimulated saliva specimens were collected to measure salivary pH thirty minutes after consumption of sucrose by mouth. Immediately after the pH measurement and oral clinical examination, the pediatric dentist provider determined for child-subjects their diagnoses for early childhood caries and severity, respectively guided by the gold-standard classifications promulgated by the American Academy of Pediatric Dentistry and International Caries Detection and Assessment System. Salivary pH of 6.0 was statistically calculated as the screening cut-off point. Statistical analyses calculated values for true positive, false positive, true negative, false negative, and the diagnostic testing accuracy metrics for prevalence, specificity, sensitivity, diagnostic odds ratio, positive and negative predictive values, positive and negative likelihood ratios, and Youden’s Index. Regression models were utilized to determine the respective odds ratio associations between child and maternal sucrose-stimulated salivary pH versus the diagnosis and severity of early childhood caries.ResultsFor early childhood caries diagnosis, child sucrose-stimulated salivary pH yielded diagnostic test accuracy metrics of 47.7 percent prevalence, 72.42 percent specificity, 59.47 percent sensitivity, 66.30 percent positive predictive value, and 66.20 percent negative predictive value, and diagnostic odds ratio 3.85. The results for maternal sucrose-stimulated salivary pH for caries severity were similar in value. Maternal sucrose-stimulated salivary pH displayed lower overall DTA metrics compared to child sucrose-stimulated salivary pH, but both child and maternal sucrose-stimulated salivary pH had higher specificity than sensitivity and displayed moderate levels of positive and negative predictive values. Child sucrose-stimulated salivary pH less than 6.0 had 3.89 times higher odds for ECC diagnosis and 3.56 times higher odds of moderate-extensive caries severity than child sucrose-stimulated salivary pH greater than 6.0. Maternal sucrose-stimulated salivary pH less than 6.0 had 1.60 times higher odds of moderate-extensive caries severity than maternal sucrose-stimulated salivary pH greater than 6.0.ConclusionChild and maternal sucrose-stimulated salivary pH screening tests are useful as a screening tool to identify children at high-risk for early childhood caries.
Crusty-Pinky: A Novel Polyextremotolerant Fungus and itsMethylobacteriumSymbionts Could be an Essential Symbiosis for the Biological Soil Crust Consortium
Authors: Carr Erin C , Saha Rajib , Harris Steven D , Riekhof Wayne R 
Published: February 2025

AbstractJF2 08-2F Crusty is a novel melanized polyextremotolerant fungus isolated from a biological soil crust, which we believe harborsMethylobacteriumspp. endosymbionts, called Pinky. Crusty is capable of utilizing many sources of carbon and nitrogen and is resistant to multiple metals and UV-C due to its melanized cell wall. We were unable to recover a Pinky-free culture of Crusty via usage of antibiotics. However, when exposed to antibiotics that kill or stop the growth of the Pinky, growth of Crusty is significantly stunted, implying that actively growing Pinky symbionts are needed for Crusty’s optimal growth. The Crusty-Pinky symbiosis also seems to be able to perform active metabolism in carbonless and nitrogenless medium, which we believe is due to Pinky’s ability to perform aerobic anoxygenic photosynthesis. Finally, Pinky was identified as being capable of growth stimulation of the algaeChlorella sorokiniana, indicating that Pinky likely produces cytokinins or auxins whichMethylobacteriumare known for. Features of this symbiosis provide us insight into the ecological roles of these microbes within the biological soil crust.
Spatial transcriptomics uncovers hybrid, pro-inflammatory and pro-fibrotic cellular niches in pulmonary granuloma of patients with chronic sarcoidosis
Authors: Christian Leonard , Yilmaz Hande , Ruwisch Jannik , Giercke Leon , Seeliger Benjamin , Kamp Jan C. , Bayraktar Sirvan , Ewen Raphael , Graalmann Theresa , Fuge Jan , Greer Mark , Ius Fabio , Welte Tobias , Hohlfeld Jens M. , Hoeper Marius M. , Gottlieb Jens , Kaminski Naftali , Prasse Antje , Jonigk Danny , Li Yang , Falk Christine , Neubert Lavinia , Schupp Jonas C. 
Published: February 2025

AbstractBackgroundSarcoidosis is a disease of unknown etiology characterized by the formation of immune cell accumulation (granuloma) in the lung and other tissues. Chronic sarcoidosis may lead to pulmonary fibrosis.AimTo unravel cellular niches within pulmonary granuloma of chronic sarcoidosis patients using spatial transcriptomics.MethodsSpatial transcriptomics using the Visium platform (10x Genomics) was performed on nine granuloma-containing lung explants from sarcoidosis patients. Validation of gene expression was performed through immunohistofluorescence protein staining and RNAin situhybridization.ResultsSpatial gene expression covered 30,587 gene expression spots and 173 granulomas. A CD68+macrophage niche was localized in the center of the granuloma, with a CD3+T and CD20+B cell niche in close proximity, surrounded by a COL3A1+fibroblast niche. In the central granuloma macrophage niche, expression of the pro-fibrotic macrophage genesSPP1,CHIT1andCHI3L1was observed, genes whose expression has recently been described for macrophages in idiopathic pulmonary fibrosis. Additionally, pro-inflammatory macrophage genes were expressed in the central granuloma niche: macrophages appear armed for lysosomal degradation and ready for phagocytosis. Inner granuloma niches showed high responsiveness to interferon gamma (IFN-γ), expressing a multitude of IFN-γ-induced genes. High collagen andCTHRC1expression were observed in granuloma fibroblasts niches, characteristics of pro-fibrotic lung remodeling. Ligand-receptor analysis identified pro-inflammatory and pro-fibrotic interactions between granuloma niches.ConclusionTaken together, macrophages in the center of the sarcoidosis granuloma form an armed-and-ready, hybrid pro-inflammatory and pro-fibrotic niche, supporting granuloma persistence through continuous IFN-γ-stimulation and fibrotic remodeling conducted by fibrotic fibroblasts surrounding the granuloma.
Dissecting the RNA binding capacity of the multi-RRM protein Rrm4 essential for endosomal mRNA transport
Authors: Stoffel Nina Kim , Sankaranarayanan Srimeenakshi , Müntjes Kira , Busch Anke , König Julian , Zarnack Kathi , Feldbrügge Michael 
Published: February 2025

AbstractRNA-binding proteins (RBPs) utilize multiple RNA-binding domains (RBDs) to engage with extensive mRNA networks. Understanding the intricate interplay of modular RBDs is essential for uncovering RBP function. Yet, how individual RBDs shape transcriptome-wide interactions remains poorly understood. Here, we dissect the roles of the three RNA recognition motifs (RRMs) in the endosomal mRNA transporter Rrm4 during polar growth ofUstilago maydis. Using a comparative mutant-based iCLIP2 approach, we disclose an extensive inventory of RRM-specific binding sites. Most binding sites are prominently governed by RRM3, however, they are not critical for function. Conversely, functionally essential binding sites are recognized by a more complex RBD interplay, involving RRM1 and/or RRM2 with partial support from RRM3. By integrating transcriptome-wide RNA binding data with transcriptomics, we pinpoint their function as regulatory RNA elements affecting mRNA abundance, linking endosomal transport to stability. The modular RNA binding of Rrm4 defines distinct RNA regulons controlling mitochondrial activity, polarity factors, and cell wall remodeling – processes critical for polar growth. These findings disclose the intricate binding modes of an RBPin vivo, emphasizing how multiple RBDs differentiate functional binding sites from accessory ones to determine mRNA fate.Graphical abstractFigure 1.
From sporulation to village differentiation: the shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia
Authors: Febinia Clarissa A. , Luqman Hirzi , Kusuma Pradiptajati , Priliani Lidwina , Lewis Joseph , Wihandani Desak Made , Pinatih Gde Ngurah Indraguna , Sudoyo Herawati , Almeida Alexandre , Malik Safarina G. , Jacobs Guy S. 
Published: February 2025

SummaryDespite established roles in human health and profound global diversity, existing gut microbiome datasets are biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a novel gut microbiome dataset from 116 Indonesian individuals representing a diverse cline from transitional hunter-gatherers to rural agricultural to urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species (15%) and subspecies-level (50%) novelty. Novel taxa are rare, often village-specific, and depleted for sporulation genes, revealing a direct link between bacterial physiology, transmission, prevalence and discovery. We reveal reduced microbial diversity associated with rural-to-urban transition, and also multi-layered patterns across taxonomic levels, including opposing trends within genera. Furthermore, community membership, over diet, is often a stronger predictor of microbiome composition. Our work highlights the interplay of host behaviour, population structure and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities
Analytical evaluation of nearly singular integrals in the heat conduction boundary integral equations with heat source
Authors: Li Tengyue , Cheng Changzheng , Wang Feiyang , Hu Zongjun , Li Jingchuan 
Published: February 2025

PurposeThere are domain integrals in the integral equations for analyzing the heat conduction with a heat source.Design/methodology/approachIn order to highlight the advantages of the boundary element method, the dual reciprocity method is introduced to transform the domain integral into the boundary integral through the special interpolation function. When the internal points near the boundary are selected as the nodes for constructing the approximating functions in the dual reciprocity method, the nearly singular integrals will occur in calculating the physical quantities of these internal points. The nearly singular integrals cannot be effectively evaluated by the Gaussian numerical integration, which will reduce the calculation accuracy of the temperature and heat flux at the internal points near the boundary. Herein, a set of analytical formulas is proposed to evaluate the nearly singular integrals in the boundary integral equations for the heat conduction problem with a heat source.FindingsThus, the accurate temperature and heat flux at the internal points closer to the boundary can be evaluated by comparing with the conventional boundary element method. The characteristic of the “boundary only” of the boundary element method is maintained for analyzing the temperature field in the heat conduction problem with a heat source.Originality/valueThe boundary-domain integral equation for the heat conduction problem with a heat source is transformed into the boundary integral equation by the dual reciprocity method. Then, the analytical algorithm is introduced to evaluate the nearly singular integral in the heat conduction boundary integral equations with a heat source. The present method retains the “boundary only” characteristic of the boundary element method and effectively evaluates the nearly singular integrals when the internal point is close to the boundary.
Effect of surface roughness on the gear performance based on the mixed-THEL model
Authors: Gu Chunxing , Sheng Xiaoli , Zhang Di 
Published: February 2025

Purpose
This paper aims to investigate the gear performance during meshing. The effects of line load, velocity and rough surfaces (kurtosis and skewness) on the lubrication characteristics and fatigue life of gears were analyzed.

Design/methodology/approach
In the mixed thermoelastohydrodynamic lubrication (TEHL) model, the distributions of pressure and film thickness are predicted using the Reynolds equation. The elastic–plastic rough contact model is used to calculate the contact force and area. To predict the fatigue life of the gears, the Dang–Van fatigue model is used to obtain the fatigue parameters under different line loads, velocities and rough surfaces.

Findings
The skewness of rough surfaces has a more significant effect on gear performance. In addition, according to fatigue parameters, it is found that when the load is too large, it leads to an increase in the probability of gear failure.

Originality/value
In this paper, a mixed TEHL model considering the effects of kurtosis and skewness is developed for the line contact to predict the mixed lubrication problem during gear meshing.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-09-2024-0356/
Extrusion bioprinting device for planar and non-planar mammalian cells and bacterial scaffolds prototyping
Authors: Aragón-Lozano Daniel , Flores-Jimenez Mariana S. , Garcia-Gonzalez Alejandro , Perfecto-Avalos Yocanxóchitl , Rho-Mas Fabian , García-Gamboa Ricardo , Fuentes-Aguilar Rita Q. , Chairez Isaac 
Published: February 2025

Purpose
This study aims to develop and validate an integrated extrusion bioprinting system that produces planar and non-planar scaffolds with embedded living material (bacteria or mammalian cells), overcoming the limitation of traditional extrusion bioprinting, where the material is deposited and cultured in planar layers.

Design/methodology/approach
The bioprinting device was constructed by modifying a fused deposition modelling 3D printer, adapting the extrusion holder for hydrogel-bioinks, going from an 8-bit architecture to a 32-bit one andad hoc updating the firmware, increasing the processing capacity and enabling accurate deposition of material. The device performance was assessed in hydrogel 3D planar and non-planar extrusion, considering different radius of curvature to form porous scaffolds, evaluating their ability to retain the designed curved geometry and the cell viability maintaining in bacterial and mammalian cells bioinks.

Findings
The viability (up to 99%) and growth of bacteria and mammalian cells embedded in the scaffolds was confirmed by confocal microscopy. The suggested bioprinting platform and procedure integrates an efficient strategy for producing hydrogel-based scaffolds, obtaining 98% resolution in planar deposition. For non-planar scaffolds, it was found that they are capable of maintaining the designed curvature even after being removed from the support, with an 88% of resolution.

Originality/value
It is reported a novel and advanced 3D extrusion bioprinting strategy for producing curved and complex scaffolds, preserving resolution and sterile conditions, introducing in addition a methodology for direct design and generation of a g-code with continuous and smooth paths, pioneering on the 3D bioprinting of bacterial bioinks.
Effects of Noise and Reward on Pupil Size and Electroencephalographic Speech Tracking in a Word‐Detection Task
Authors: Iotzov Ivan , Parra Lucas C. 
Published: February 2025

ABSTRACTSpeech is hard to understand when there is background noise. Speech intelligibility and listening effort both affect our ability to understand speech, but the relative contribution of these factors is hard to disentangle. Previous studies suggest that speech intelligibility could be assessed with EEG speech tracking and listening effort via pupil size. However, these measures may be confounded, because poor intelligibility may require a larger effort. To address this, we developed a novel word‐detection paradigm that allows for a rapid behavioural assessment of speech processing. In this paradigm, words appear on the screen during continuous speech, similar to closed captioning. In two listening experiments with a total of 51 participants, we manipulated intelligibility by changing signal‐to‐noise ratios (SNRs) and modulated effort by varying monetary reward. Increasing SNR improved detection performance along with EEG speech tracking. Additionally, we find that pupil size increases with increased SNR. Surprisingly, when we modulated both reward and SNR, we found that reward modulated only pupil size, whereas SNR modulated only EEG speech tracking. We interpret this as the effects of arousal and listening effort on pupil size and of intelligibility on EEG speech tracking. The experimental paradigm developed here may be beneficial when assessing hearing devices in terms of speech intelligibility and listening effort.
Tonic Electrical Stimulation of the Locus Coeruleus Enhances Cortical Sensory‐Evoked Responses via Noradrenaline α1 and β Receptors
Authors: Suzuki Takanobu , Nagasaka Kazuaki , Otsuki Tomofumi , Otsuru Naofumi , Onishi Hideaki 
Published: February 2025

ABSTRACTThe locus coeruleus (LC) neurons send extensive projections to the somatosensory cortex and release noradrenaline (NA) at synaptic terminals, which is thought to regulate the activation of sensory‐related cells by acting on three types of receptors (α1, α2 and β). Although previous studies have examined the effects of LC stimulation on single‐unit sensory neurons, their impact on somatosensory evoked potentials (SEPs) and their temporal variations, as well as the specific roles of NA receptors, remain unclear. Herein, we investigated how SEPs are modulated by tonic LC stimulation at physiological frequencies (0.1, 1 and 4 Hz) and identified the receptors involved in these changes. Forepaw stimulation‐induced amplitudes in SEP were enhanced in response to 1 Hz stimulation of the LC but not in response to 0.1 and 4 Hz stimulation. Interestingly, the enhancement of SEPs after LC stimulation persisted for tens of minutes following the cessation of stimulation. Optical imaging using a voltage‐sensitive dye showed an increase in the depolarizing response in the somatosensory cortex after 1 Hz stimulation. Prazosin (α1 receptor antagonist) and propranolol (β receptor antagonist) inhibited SEP enhancement following 1 Hz LC stimulation, whereas yohimbine (α2 receptor antagonist) had no effect. This suggests that the enhancement in SEP observed is primarily mediated by the activation of cortical excitatory α1 and β receptors. These findings provide insight into the impact of the NA system on sensory information processing and the pathophysiology of sensory disorders related to the disruption of the NA system.
Exploring Care Home Workers' Perceptions of Implementing ECHO: A Qualitative Study
Authors: Beattie Michelle , Muirhead Kevin , Carey Nicola 
Published: February 2025

ABSTRACTBackgroundTo ensure older people living in care homes receive optimal care, care home workers (CHWs) require access to specialist support and education. Extension for Community Healthcare Outcomes (ECHO) uses existing videoconferencing to connect CHWs to specialists using case‐based learning. There is evidence in other settings to suggest that ECHO can improve practitioner knowledge and patient outcomes. There is a dearth of evidence regarding strategies for effective implementation of ECHO with CHWs.AimTo establish the experiences of ECHO, and the barriers and enablers to implementation, from the perspective of CHWs in Scotland.MethodsQualitative online focus groups (n = 4) with CHWs (n = 13) who had participated in at least one care home ECHO session and with facilitators/presenters (n = 6). Transcripts were thematically analysed.FindingsFindings were grouped into three areas: perceived impact, inhibitors and enablers. CHWs reported the positive impact of ECHO including key benefits to enhance residents' care, satisfaction with the sessions and feeling valued. Inhibitors included limited digital skills, workforce challenges and the pitch and duration of ECHO sessions. Enablers included administrative and technical support, scheduling and the structure of the ECHO approach.ConclusionsECHO allows CHWs to access specialist support, enabling learning and development, with the potential to improve residents' care. Benefits to residents' care included CHWs' enhanced understanding of choices around death and dying, and insights and understanding of causation of challenging behaviours in older people and how to manage these. Adaptations to ECHO to suit a care home context are recommended.Implications for PracticeCHWs require technical support to build competence and confidence in IT skills. This study highlights the potential for ECHO to support CHWs to access specialist support and learning for older adults in a care home context.
Comparison of dermal and eschar fibroblasts in full skin equivalents
Authors: Kutluoğlu Gizem Coşar , Vlig Marcel , Elgersma Anouk , Boekema Bouke K. H. L. , Daamen Willeke F. , Doberenz Claudia , Manikowski Dominique 
Published: February 2025

AbstractFull‐thickness burn wounds pose significant problems, demanding specialised therapies to avoid complications and promote recovery. Eschar tissue, which forms in response to severe burns, contains viable fibroblasts, which migrate from the surrounding tissue in response to burn injury and exhibit a myofibroblast phenotype. The goal of this study was to characterise eschar‐derived fibroblasts and examine their use for engineered in vitro full skin equivalents in comparison to normal dermal fibroblasts, which were harvested from non‐injured skin. Microarray analysis indicated that eschar fibroblasts differ from dermal fibroblasts in various biological processes including inflammation, extracellular matrix formation, cell migration and differentiation. Skin equivalents with eschar fibroblasts showed similarities to those generated using normal dermal fibroblasts in terms of epidermis and dermis formation. However, in contrast to dermal fibroblast‐based full skin equivalents, eschar fibroblast‐based equivalents exhibited macroscopic contractile behaviour. In addition, eschar fibroblasts‐based equivalents demonstrated higher alpha‐smooth muscle actin expression on mRNA and protein levels. In conclusion, our findings suggest that eschar fibroblasts‐based full skin equivalents hold promise as a platform to study burn wound environments as eschar fibroblasts are clinically more relevant fibroblasts and able to mimic certain aspects of the challenging wound environment in vitro.