bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proposal ofPatescibacterium danicumgen. nov., sp. nov. in the ubiquitous ultrasmall bacterial phylumPatescibacteriotaphyl. nov.
Authors: Dutkiewicz Zuzanna , Singleton Caitlin Margaret , Sereika Mantas , Villada Juan C. , Mussig Aaron J. , Chuvochina Maria , Albertsen Mads , Schulz Frederik , Woyke Tanja , Nielsen Per Halkjær , Hugenholtz Philip , Rinke Christian 
Published: November 2024

AbstractCandidatusPatescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities and dependence on other prokaryotic hosts. Despite the prevalence of the nameCa.Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes (ICNP) and lacks a nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes (MAGs) and by proposing one of them (ABY1TS) to serve as the nomenclatural type for the speciesPatescibacterium danicumTSgen. nov., sp. nov. according to the rules of the SeqCode. Rank-normalized phylogenomic inference confirmed the stable placement ofP. danicumTSin the class ABY1 withinCa.Patescibacteria. Based on these results, we proposePatescibacteriumgen. nov. to serve as the type genus for associated higher taxa, including the phylumPatescibacteriotaphyl. nov. We complement our proposal with a genomic characterization, metabolic reconstruction, and biogeographical analysis ofPatescibacterium. Our results confirm small genome sizes (< 1Mbp), low GC content (>36%), and the occurrence of long gene coding insertions in the 23S rRNA sequences, along with reduced metabolic potential, inferred symbiotic lifestyle, and a global distribution. In summary, this effort, focused on the fourth-largest phylum in the bacterial domain, aims to provide nomenclatural stability in the scientific literature.
The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation
Authors: Ranjan Amitabh , Mattijssen Sandy , Charlly Nithin , Cruz Gallardo Isabel , Pitman Leah F. , Coleman Jennifer C. , Conte Maria R. , Maraia Richard J. 
Published: November 2024

ABSTRACTLARP4 interacts with poly(A)-binding protein (PABP) to protect mRNAs from deadenylation and decay, and recent data indicate it can direct the translation of functionally related mRNA subsets. LARP4 was known to bind RACK1, a ribosome-associated protein, although the specific regions involved, and relevance had been undetermined. Here, yeast two-hybrid domain mapping followed by other methods identified positions 615-625 in conserved region-2 (CR2) of LARP4 (and LARP4B) as directly binding RACK1 region 200-317. Consistent with these results, AlphaFold2-multimer predicted high confidence interaction of CR2 with RACK1 propellers 5-6. CR2 mutations strongly decreased LARP4 association with cellular RACK1 and ribosomes by multiple assays, whereas less effect was observed for PABP association, consistent with independent interactions. CR2 mutations decreased LARP4 ability to optimally stabilize a β-globin mRNA reporter containing an AU-rich element (ARE) more significantly than a β-globin and other reporters lacking this element. While polysome profiles indicate the β-glo-ARE mRNA is inefficiently translated, consistent with published data, we show that LARP4 increases its translation whereas the LARP4-CR2 mutant is impaired. Analysis of nanoLuc-ARE mRNA for production of luciferase activity confirmed LARP4 promotes translation efficiency while CR2 mutations are disabling. Thus, LARP4 CR2-mediated interaction with RACK1 can promote translational efficiency of some mRNAs.
Explicit derivation of the standard fitting technique for two-state protein transitions using differential scanning calorimetry data
Authors: Priklopil Tadeas 
Published: November 2024

AbstractThis paper has three main objectives. First, we aim to derive from first principles a linear heat capacity model for proteins exhibiting two-state conformational transition dynamics, which includes, as a special case, the constant heat capacity model frequently referenced in the literature. Second, we present a protocol for inferring the Gibbs free energy of protein folding by fitting the linear heat capacity model to differential scanning calorimetry data. Third, we demonstrate this protocol using Mathematica software, applying it to real datasets and comparing the linear and constant heat capacity models. While most of our derivations are well established in the literature, we provide a step-by-step bridge from mathematical modeling to application, addressing a practical gap in existing resources that benefits researchers.
High throughput single-cell proteomics of in-vivo cells
Authors: Karagach Shiri , Smollich Joachim , Atrakchi Ofir , Mohan Vishnu , Geiger Tamar 
Published: November 2024

AbstractSingle-cell mass spectrometry-based proteomics (SCP) can resolve cellular heterogeneity in complex biological systems and provide a system-level view of the proteome of each cell. Major advancements in SCP methodologies have been introduced in recent years, providing highly sensitive sample preparation methods and mass spectrometric technologies. However, most studies present limited throughput and mainly focus on the analysis of cultured cells. To enhance the depth, accuracy, and throughput of SCP for tumor analysis, we developed an automated, high-throughput pipeline that enables the analysis of 1,536 single cells in a single experiment. This approach integrates low-volume sample preparation, automated sample purification, and LC-MS analysis with the Slice-PASEF method. Integration of these methodologies into a streamlined pipeline led to a robust and reproducible identification of more than 3000 proteins per cell. We applied this pipeline to analyze tumor macrophages in a murine lung metastasis model. We identified over 1,800 proteins per cell, including key macrophage markers and ∼500 differentially expressed proteins between tumor and control macrophages. PCA analysis successfully separated these populations, revealing the utility of SCP in capturing biologically relevant signals in the tumor microenvironment. Our results demonstrate a robust and scalable pipeline poised to advance single-cell proteomics in cancer research.
Within-plant variation in chemical defence ofErysimum cheiranthoidesdoes not explainPlutella xylostellafeeding preference
Authors: Wang Kunqi , Züst Tobias 
Published: November 2024

AbstractPlants invest a substantial fraction of their resources into defence against herbivores, with the highest levels of defence often allocated only to the most valuable tissues. Plants in the genusErysimum(Brassicaceae) evolved the ability to produce novel cardenolides in addition to ancestrally conserved glucosinolates. While plants co-express both defences, differences in tissue-specific expression might represent an effective cost saving strategy.Larvae of the glucosinolate-resistant diamondback mothPlutella xylostellaoccasionally feed onErysimum cheiranthoidesbut tend to avoid younger leaves. Here, we predicted that caterpillar feeding preference is shaped by variation in cardenolide levels, thus we quantified within-plant variation in defensive and nutritional traits of vegetative or early reproductive plants and performed feeding assays to evaluate the relative importance of cardenolides.In accordance with optimal defence theory (ODT), youngest leaves contained the most nutrients and the highest levels of cardenolides, glucosinolates, and trichomes, with more extreme within-plant differences found in reproductive plants. Caterpillars consistently avoided the well-defended youngest leaves both on whole plants and with detached leaf discs. Surprisingly, neither experimental addition (by external application) nor removal (by CRISPR-Cas9 knockout) of cardenolides significantly affected caterpillar feeding preference.Physical and chemical defences, including cardenolides, co-vary withinE. cheiranthoidesto maximise defence of youngest leaves. WhileP. xylostellaclearly responds to some of these traits, the prominent cardenolide defence appears to lack potency against this specialist herbivore. Nonetheless, the careful regulation and re-mobilization of cardenolides to younger leaves during plant development suggests an important role for plant functioning.One-sentence summaryDistribution of ancestral and novel defensive chemicalsErysimum cheiranthoidesvary within plant according to relative leaf value and leaf age, but in isolation, chemical defences are insufficient to affect feeding preference ofPlutella xylostellalarvae.
Defective Neurogenesis in Lowe Syndrome is Caused by Mitochondria Loss and Cilia-related Sonic Hedgehog Defects
Authors: Lo Chien-Hui , Chen Siyu , Zhao Jingyu , Liu Zhiquan , Wang Biao , Wang Qing , Kowal Tia J. , Sun Yang 
Published: November 2024

AbstractHuman brain development is a complex process that requires intricate coordination of multiple cellular and developmental events. Dysfunction of lipid metabolism can lead to neurodevelopmental disorders. Lowe syndrome (LS) is a recessive X-linked disorder associated with proximal tubular renal disease, congenital cataracts and glaucoma, and central nervous system developmental delays. Mutations in OCRL, which encodes an inositol polyphosphate 5-phosphatase, lead to the development of LS. The cellular mechanism responsible for neuronal dysfunction in LS is unknown. Here we show depletion of mitochondrial DNA and decrease in mitochondrial activities result in neuronal differentiation defects. Increased astrocytes, which are secondary responders to neurodegeneration, are observed in neuronal (iN) cells differentiated from Lowe patient-derived iPSCs and an LS mouse model. Inactivation of cilia-related sonic hedgehog signaling, which organizes the pattern of cellular neuronal differentiation, is observed in an OCRL knockout, iN cells differentiated from Lowe patient-derived iPSCs, and an LS mouse model. Taken together, our findings indicate that mitochondrial dysfunction and impairment of the ciliary sonic hedgehog signaling pathway represent a novel pathogenic mechanism underlying the disrupted neuronal differentiation observed in LS.
Neural synchrony is “good enough” for speech comprehension
Authors: Rafferty M. Blake , Brown Edward C. , Casenhiser Devin M. 
Published: November 2024

AbstractRecent evidence indicates that neural populations exhibit synchronous firing at phrase boundaries to facilitate the encoding of syntactic units during speech comprehension. However, good-enough processing accounts of speech comprehension suggest that detailed syntactic analysis may not always be necessary for successful interpretation, especially when listeners can deduce meaning from lexical-semantic contexts. In this brief report, we evaluate this notion and assess whether neural synchrony to syntactic boundaries is modulated by local lexical-semantic content. To this end, we reanalyzed an open-source EEG dataset, consisting of brain recordings obtained while participants passively listened to an audiobook. To determine neural synchrony to phrase boundaries, we computed mutual information (MI) between delta band EEG activity (< 3Hz) and hierarchically derived syntactic structures for each sentence in the audiobook. We then quantified local-lexical semantic contexts using semantic dissimilarity values that were derived from high-dimensional vectors of co-occurrence. We then regressed MI values for each sentence against the sentence’s semantic dissimilarity values, using linear mixed-effects models. Results indicated that neural synchrony to phrase boundaries showed a positive linear relationship with semantic dissimilarity. We interpret this finding as evidence that listeners’ reliance on syntactic information during speech comprehension is modulated by local lexical-semantic contexts, consistent with good-enough processing accounts.
Genome sizes of animal RNA viruses reflect phylogenetic constraints
Authors: Takada Kosuke , Holmes Edward C. 
Published: November 2024

AbstractAnimal genomes are characterized by extensive variation in size. RNA viruses similarly exhibit substantial genomic diversity, with genome lengths ranging from 1.7 to 64 Kb. Despite the myriad of novel viruses discovered by metagenomics, we know little of the factors that shape the evolution of the genome size in RNA viruses. We analyzed the variation in genome sizes across orders and families of animal RNA viruses. We found that RNA viruses can have highly variable genome sizes within and among orders, with theNidovirales(including theCoronaviridae) having both significantly larger genomes and a greater range of genome sizes than other orders. In theBunyavirales, Amarillovirales, NidoviralesandPicornaviralesthe genome sizes of invertebrate-associated RNA viruses were significantly larger than those that infect vertebrates, in contrast to their animal hosts in which vertebrates commonly have larger genomes than invertebrates. However, in theMononegavirales, vertebrate viruses were significantly larger than those viruses associated with invertebrates. There were similarly complex associations between genome size and patterns of genome segmentation. In theBunyavirales, Reovirales, andNidovirales, viruses with segmented genomes or that possessed a large number of segments, had significantly larger genome sizes that viruses with non-segmented genomes or a small number of segments, while in theArticulaviralesthere were no significant differences in genome size among viruses possessing any number of genome segments. More broadly, our analysis revealed that taxonomic position (i.e., RNA virus order) had a greater impact on genome size than whether viruses infected vertebrates or invertebrates or their pattern of genome segmentation. Hence, the phylogenetic constraints on genome size are of sufficient magnitude to shape other aspects of virus evolution.
Marketing and communication in the wine sector: the Catalan wine DO on social networks
Authors: Mundet Pons Jordi , Bustos Díaz Javier , Molleví Bortoló Gemma 
Published: November 2024

PurposeThis paper aims to analyze the social media strategies of wineries from three quality Denominations of Origin (DOs): Alella, Empordà and Priorat (Spain). It explores how digitalization has become a crucial element in contemporary marketing communication strategies and examines the presence and use of social media by these wineries.Design/methodology/approachThe study employs a quantitative methodology to identify the most commonly used social media platforms among the selected DOs. Additionally, a content analysis is conducted to understand the themes these DOs use to engage with their audience. The analysis focuses on the social media presence and content strategies of the wineries within the specified DOs.FindingsThe study reveals that an increased understanding and utilization of new technologies by local citizens could enhance the digital development of these wineries. The research identifies the prevalent social media platforms used by the DOs and examines the content themes that wineries use to connect with their audience.Research limitations/implicationsThe findings emphasize the need to improve digital literacy among local communities to support the digital growth of wineries. The study also highlights the importance of understanding which social media platforms and content themes are most effective for engaging target audiences. Future research could explore the impact of specific digital strategies on business performance and consumer engagement.Originality/valueThis research contributes to the understanding of social media strategies in the wine industry, particularly within Catalan DOs, by providing insights into the use of digital tools and content themes in winery marketing.
Availability and cost of gluten-free products in Algeria
Authors: Bouasla Abdallah , Saouchi Sonia , Benramoul Khaoula , Vriesekoop Frank 
Published: November 2024

PurposeA strict gluten-free diet (GFD) is the only effective treatment for coeliac disease (CD), which has an increasing prevalence. However, the limited availability and high price of gluten-free products (GFPs) compared to their gluten-containing counterparts (GCCs) are still among the factors that may influence compliance with a strict GFD. The purpose of this study is to assess the availability and price of GFPs in retail stores in a major Algerian city and investigate how they compare to GCCs.Design/methodology/approachWe performed a cross-sectional study that targets a representative number of supermarkets and grocery stores in Constantine (Algeria). All available GFPs as well as their GCCs were recorded. The price per 100 g was recorded for each product.FindingsAmong the 285 visited stores, only 25.4% of them sold GFPs, which were more available at supermarkets than at grocery stores. The category “gluten-free pasta and couscous” was the most represented (43.8%). A total of 64 GFPs were observed across 285 stores investigated, and their price was two to six times higher than that of their GCCs.Originality/valueThis study showed the limited availability and diversity and higher price of processed GFPs in Algeria. This negatively influences compliance with GFD as well as the quality of life of patients with CD. Furthermore, the findings prompt the national government to provide financial support to coeliac individuals.
How the Soybean Producer Subsidy Policy affects crop planting structure: evidence from Chinese county-level data
Authors: Zhang Siqi , Cai Rong , Liang Xintong , Zhang Weifu 
Published: November 2024

PurposeThe Soybean Producer Subsidy Policy (SPSP), an agricultural support policy enacted in China within the past few years, is designed to optimise crop planting structure. This study analyses the impact of SPSP on the crop planting structure in terms of absolute and comparative incomes and elucidates the mechanisms involved.Design/methodology/approachUtilising balanced county-level panel data from 966 counties in China’s major soybean-producing regions, spanning from 2008 to 2021, we investigate the impacts of SPSP on crop planting structure by applying a difference-in-difference (DID) model.FindingsThe findings reveal several crucial insights. First, SPSP optimises the crop planting structure in Northeast China, primarily through an expansion in the area sown to soybeans and a simultaneous reduction in the area sown to maize. Second, the impacts of SPSP gradually strengthen over time but begin to weaken by 2021. Third, heterogeneity analysis indicates that the effects of SPSP are most pronounced in Eastern Inner Mongolia, followed by Heilongjiang, Jilin, and Liaoning. Finally, SPSP incentivises farmers to expand soybean sown areas by improving absolute rather than comparative incomes from soybean cultivation.Practical implicationsAddressing structural contradictions within China’s food supply chain necessitates the adjustment of support policies for different crops to mitigate market distortions. Establishing a holistic agricultural support system encompassing various crops could promote sustainable agricultural practices in the future.Originality/valueOur findings are valuable for policy makers in China and globally who aim to establish support systems for regional linkages that include a variety of crops.
Two-stage algorithm for automatic repair of pavement cracks
Authors: Yu Jing , Guo Jiawei , Zhang Qi , Xing Lining , Lv Songtao 
Published: November 2024

PurposeTo develop an automated system for identifying and repairing cracks in asphalt pavements, addressing the urgent need for efficient pavement maintenance solutions amidst increasing workloads and decreasing budgets.Design/methodology/approachThe research was conducted in two main stages: Crack identification: Utilizing the U-Net deep learning model for pixel-level segmentation to identify pavement cracks, followed by morphological operations such as thinning and spur removal to refine the crack trajectories. Automated crack repair path planning: Developing an enhanced hybrid ant colony greedy algorithm (EAC-GA), which integrates the ant colony (AC) algorithm, greedy algorithm (GA) and three local enhancement strategies – PointsExchange, Cracks2OPT and Nearby Cracks 2OPT – to plan the most efficient repair paths with minimal redundant distance.FindingsThe EAC-GA demonstrated significant advantages in solution quality compared to the GA, the traditional AC and the AC-GA. Experimental validation on repair areas with varying numbers of cracks (16, 26 and 36) confirmed the effectiveness and scalability of the proposed method.Originality/valueThe originality of this research lies in the application of advanced deep learning and optimization algorithms to the specific problem of pavement crack repair. The value is twofold: Technological innovation in the field of pavement maintenance, offering a more efficient and automated approach to a common and costly issue. The potential for significant economic and operational benefits, particularly in the context of reduced maintenance budgets and increasing maintenance demands.
The impact of environmental, social and governance (ESG) performance on the duration of dividend sustainability: a survival analysis
Authors: Liu Yen-Yu , Lee Pin-Sheng 
Published: November 2024

PurposeThis study investigates the impact of ESG performance on the duration of dividend sustainability, introducing survival analysis as a novel methodological approach in this context and highlighting its differences from commonly used regression analyses such as OLS and logistic regression.Design/methodology/approachSurvival analysis methods, including Kaplan–Meier estimates and Cox proportional hazards time-dependent regression, were employed to examine data from publicly listed companies in Taiwan between 2016 and 2023. Additionally, logistic regression was tested to compare results with those from the survival analysis.FindingsWhile overall ESG performance did not show a significant impact on the duration of dividend sustainability, a detailed analysis of the individual ESG components revealed that the environmental performance component can extend the duration of dividend sustainability.Research limitations/implicationsThe findings based on companies in Taiwan may not generalize to other contexts. However, this study primarily highlights the application of survival analysis in ESG-related literature. Future research could explore similar analyses in different international settings to better understand the broader applicability of these results.Practical implicationsThe results suggest that the impact of ESG performance on dividend amounts and the duration of dividend sustainability are distinct issues. Investors and stakeholders should consider these differences when assessing corporate performance and making investment decisions.Social implicationsThe study highlights the importance of environmental sustainability in corporate dividend policies, indicating that companies with better environmental performance provide more stable returns.Originality/valueThis study introduces survival analysis to the study of ESG performance and the duration of dividend sustainability, addressing a gap in the literature by focusing on the duration of dividends rather than their amount.