bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic risk of inflammatory bowel disease is associated with disease course severity
Authors: Vestergaard Marie Vibeke , Allin Kristine Højgaard , Nøhr Anne Krogh , Lominchar Jesus Vicente Torresano , Christensen Heidi Søgaard , Krarup Henrik , Nielsen Kaspar René , Jacobsen Henrik Albæk , Bybjerg-Grauholm Jonas , Bækvad-Hansen Marie , Brøndum Rasmus Froberg , Bøgsted Martin , Larsen Lone , Sazonovs Aleksejs , Jess Tine
Published: November 2024

Background

Genetic susceptibility to inflammatory bowel disease (IBD) has been widely studied, whereas the genetic contribution to disease progression over time remains largely unknown. In a unique population-based cohort, we explored if genetic susceptibility to IBD associated with disease course severity.

Methods

In a Danish nationwide cohort of 3688 patients with Crohn’s disease (CD), 4491 patients with ulcerative colitis (UC), and 9469 controls, we estimated polygenic scores (PGS) for IBD susceptibility. We then investigated the association between susceptibility PGS and severe versus less severe disease courses. Patients were categorized as having a severe disease course if needing I) at least two IBD-related hospitalizations exceeding two days, II) at least two IBD-related major surgeries, III) one hospitalization and one major surgery not overlapping in time, or IV) total use of minimum 5000 mg systemic corticosteroids within the first three years of diagnosis. Secondary analyses explored the association with other severity measures including inflammatory markers, exposure to biologics and immunomodulators, and time to hospitalization and major IBD-related surgery. Statistical analyses included logistic, linear, and Cox proportional hazards regression, and predictive modeling using random forest.

Findings

Patients with severe disease courses had higher susceptibility PGS than patients with less severe disease courses (CD: OR=1·27,P=7·73×10−10, UC: OR=1·35,P=7·29×10−17per SD increase in susceptibility PGS). When comparing the highest versus lowest PGS quintile, we observed a hazard ratio (HR) for major surgery of 2·74 (P=7·19×10−18) in patients with CD and 2·04 (P=4·36×10−7) in patients with UC. A higher susceptibility PGS was also associated with longer and more frequent hospitalizations, higher levels of C-reactive protein, decreased hemoglobin, and a higher need for corticosteroids, immunomodulators, and biologic therapies.

Interpretation

Patients with a higher genetic burden for developing IBD also experience a more severe disease course, suggesting a shared genetic architecture between disease susceptibility and severity.

Funding

Danish National Research Foundation, DNRF148, Lundbeck Foundation, R313-2019-857, Novo Nordisk Foundation, NNF23OC0087616, Danish Colitis Crohn Association.
Nowcasting epidemic trends using hospital- and community-based virologic test data
Authors: Lim Tse Yang , Kanjilal Sanjat , Doron Shira , Penney Jessica , Haddix Meredith , Koo Tae Hee , Danza Phoebe , Fisher Rebecca , Grad Yonatan H. , Hay James A.
Published: November 2024

Epidemiological surveillance typically relies on reported incidence of cases or hospitalizations, which can suffer significant reporting lags, biases and under-ascertainment. Here, we evaluated the potential of viral loads measured by RT-qPCR cycle threshold (Ct) values to track epidemic trends. We used SARS-CoV-2 RT-qPCR results from hospital testing in Massachusetts, USA, municipal testing in California, USA, and simulations to identify predictive models and covariates that maximize short-term epidemic trend prediction accuracy. We found SARS-CoV-2 Ct value distributions correlated with epidemic growth rates under real-world conditions. We fitted generalized additive models to predict log growth rate or direction of reported SARS-CoV-2 case incidence using features of the time-varying population Ct distribution and assessed the models’ ability to track epidemic dynamics in rolling two-week windows. Observed Ct value distributions accurately predicted epidemic growth rates (growth rate RMSE ∼ 0.039-0.052) and direction (AUC ∼ 0.72-0.78). Performance degraded during periods of rapidly changing growth rate. Predictive models were robust to testing regimes and sample sizes; accounting for population immunity or symptom status yielded no substantial improvement. Trimming Ct value outliers improved performance. These results indicate that analysis of Ct values from routine PCR tests can help monitor epidemic trends, complementing traditional incidence metrics.
Phenotype Scoring of Population Scale Single-Cell Data Dissects Alzheimer’s Disease Complexity
Authors: He Chenfeng , Li Athan Z. , Arachchilage Kalpana Hanthanan , Gupta Chirag , Huang Xiang , Zhao Xinyu ,   PsychAD Consortium, Girdhar Kiran , Voloudakis Georgios , Hoffman Gabriel E. , Bendl Jaroslav , Fullard John F. , Lee Donghoon , Roussos Panos , Wang Daifeng
Published: November 2024

The complexity of Alzheimer’s disease (AD) manifests in diverse clinical phenotypes, including cognitive impairment and neuropsychiatric symptoms (NPSs). However, the etiology of these phenotypes remains elusive. To address this, the PsychAD project generated a population-level single-nucleus RNA-seq dataset comprising over 6 million nuclei from the prefrontal cortex of 1,494 individual brains, covering a variety of AD-related phenotypes that capture cognitive impairment, severity of pathological lesions, and the presence of NPSs. Leveraging this dataset, we developed a deep learning framework, called Phenotype Associated Single Cell encoder (PASCode), to score single-cell phenotype associations, and identified ∼1.5 million phenotype associate cells (PACs). We compared PACs within 27 distinct brain cell subclasses and prioritized cell subpopulations and their expressed genes across various AD phenotypes, including the upregulation of a reactive astrocyte subtype with neuroprotective function in AD resilient donors. Additionally, we identified PACs that link multiple phenotypes, including a subpopulation of protoplasmic astrocytes that alter their gene expression and regulation in AD donors with depression. Uncovering the cellular and molecular mechanisms underlying diverse AD phenotypes has the potential to provide valuable insights towards the identification of novel diagnostic markers and therapeutic targets. All identified PACs, along with cell type and gene expression information, are summarized into an AD-phenotypic single-cell atlas for the research community.
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

CandidatusPatescibacteria 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

LARP4 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

This 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

Single-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.
Consolidation of Sequential Planning
Authors: Vikbladh Oliver M. , Russek Evan M. , Burgess Neil
Published: November 2024

Thriving in changing environments requires the capacity to evaluate novel courses of action. This ability is hypothesized to depend on sequential planning via step-by-step simulations of the future, using cognitive maps or schemas of task contingencies. However, it is still unclear if, how and where in the brain such flexible planning is enacted. In parallel, it is thought that consolidation transforms memory representations over time to promote adaptive behaviour. Here, we hypothesize that consolidation strengthens cognitive maps of task contingencies used for simulation during sequential planning. To test this, we developed a novel behavioural task and a new multivariate method for analysis of magnetoencephalography (MEG) data. Using choice and reaction time data we dissociated flexible sequential planning from alternative non-sequential strategies, and identified this behaviour with robust neural markers of step-by-step simulation, localized to the anterior medial temporal lobe. Retesting a week later we showed that consolidation enhanced sequential planning and strengthened markers of sequential simulation in the prefrontal cortex, consistent with systems consolidation theory. By revealing that consolidation improves future simulations for flexible planning we open up a new frontier for the investigation of the functional interactions between memory and decision-making.
Sharing the Spotlight: Uncovering common attentional dynamics across species
Authors: Glukhova Mina , Tlaie Alejandro , Muresan Raul , Taylor Robert , Ferracci Pierre-Antoine , Shapcott Katharine , Arne Olga , Ciuparu Andrei , Havenith Martha Nari , Schölvinck Marieke Louise
Published: November 2024

Sustained attention is a key underlying process to many natural behaviours that are shared by multiple species. Yet the way it is commonly studied in a lab context precludes any meaningful cross-species comparisons. Here, we engaged mice, monkeys, and humans in the exact same, natural perceptual decision task in a VR environment. We captured their behaviour into several parameters along the speed/accuracy axes along which sustained attention is classically defined, and used HMMs to infer four attentional states. We show that the dynamics of these states, both in terms of their durations as well as the transitions between them, are much more similar between the species than might have been expected. Moreover, attentional state fluctuations seem to be internally generated. The task and analyses developed here represent a new approach to comparing sustained attention across species in an objective, data-driven way.
Within-plant variation in chemical defence ofErysimum cheiranthoidesdoes not explainPlutella xylostellafeeding preference
Authors: Wang Kunqi , Züst Tobias
Published: November 2024

Plants 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 summary

Distribution 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

Human 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.
Cognitive network interactions through communication subspaces in large-scale models of the neocortex
Authors: Pereira-Obilinovic Ulises , Froudist-Walsh Sean , Wang Xiao-Jing
Published: November 2024

The neocortex-wide neural activity is organized into distinct networks of areas engaged in different cognitive processes. To elucidate the underlying mechanism of flexible network reconfiguration, we developed connectivity-constrained macaque and human whole-cortex models. In our model, within-area connectivity consists of a mixture of symmetric, asymmetric, and random motifs that give rise to stable (attractor) or transient (sequential) heterogeneous dynamics. Assuming sparse low-rank plus random inter-areal connectivity, we show that our model captures key aspects of the cognitive networks' dynamics and interactions observed experimentally. In particular, the anti-correlation between the default mode network and the dorsal attention network. Communication between networks is shaped by the alignment of long-range communication subspaces with local connectivity motifs and is switchable in a bottom-up salience-dependent routing mechanism. Furthermore, the frontoparietal multiple-demand network displays a coexistence of stable and dynamic coding, suitable for top-down cognitive control. Our work provides a theoretical framework for understanding the dynamic routing in the cortical networks during cognition.
Neural synchrony is “good enough” for speech comprehension
Authors: Rafferty M. Blake , Brown Edward C. , Casenhiser Devin M.
Published: November 2024

Recent 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

Animal 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

Purpose

This 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/approach

The 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.

Findings

The 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/implications

The 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/value

This 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

Purpose

A 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/approach

We 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.

Findings

Among 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/value

This 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

Purpose

The 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/approach

Utilising 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.

Findings

The 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 implications

Addressing 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/value

Our 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

Purpose

To 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/approach

The 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.

Findings

The 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/value

The 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

Purpose

This 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/approach

Survival 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.

Findings

While 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/implications

The 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 implications

The 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 implications

The study highlights the importance of environmental sustainability in corporate dividend policies, indicating that companies with better environmental performance provide more stable returns.

Originality/value

This 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.
Interspecific trait differences drive plant community responses on serpentine soils
Authors: Delhaye Guillaume , Dimitrakopoulos Panayiotis G. , Adamidis George C.
Published: November 2024

Serpentine ecosystems are characterised by multiple environmental stressors: high levels of trace metals such as nickel (Ni), low availability of macronutrients and low water retention. These harsh environmental conditions exert a strong selective force on the vegetation, but their effect on community assembly processes and the functional trait composition remains unknown.

In 26 plots on four serpentine sites on Lesbos Island (Greece), we measured six leaf functional traits related to resource acquisition and stress resistance on the 20 most abundant plant species. We quantified the proportion of variance explained by inter‐ and intraspecific trait differences and tested if individual species showed changes in trait values explained by soil Ni content. We investigated the adaptive value and the community level changes for each trait along the natural soil Ni gradient using a mixed model approach and functional diversity analyses. We tested the role of the abundant serpentine endemic and Ni‐hyperaccumulating species Odontarrhena lesbiaca in driving these patterns.

Intraspecific variation explained by soil Ni content is smaller than 4%, and most of the variance is explained by interspecific differences in trait values. Most species do not show significant changes in trait values in response to soil Ni. At the community level, low specific leaf areas, small and thick leaves are selected on high Ni soils. Functional diversity analyses suggest a shift towards a stress tolerance syndrome (thick and small leaves with low SLA values) and an increase in functional diversity on Ni‐rich soils. However, these patterns are driven by the increasing abundance of O. lesbiaca.

The endemic Ni hyperaccumulator has a stress tolerance strategy with small thick leaves and low SLA, while the community of broadly distributed species show an increase in trait values related to dominance and fast growth.

Synthesis. Intraspecific variation in leaf trait responds little to soil metal toxicity. Endemic species harbour unique trait values compared to species with broad distribution which should justify their conservation as a priority.
Persian version of the McHale co‐parenting scale: The evaluation of the psychometric properties
Authors: Kaviyani Faezeh , Saadati Hasan , Bahreinian Seyed Abdolmajid
Published: November 2024

Validation of the MacHale Co‐parenting Scale (1997) was examined in a sample of 192 Persian‐speaking parents who had children in primary school. Translation of this scale was performed using the forward–backward method. To assess reliability, internal consistency was used after translating the items into Persian. Face validity, content validity and structural validity were also applied to ensure tool validity. The results indicated that Ballit's sphericity test yielded a value of 1153.138 at a significance level of p < .05. Using varimax rotation, three factors (Family Integrity, Consistency and Conflict) were identified with eigenvalues greater than 1 and factor loadings higher than 0.5. The total factors explained 58.18 per cent of the variance in the data. Additionally, the Cronbach's alpha coefficient for the entire questionnaire was 0.84. The Persian version of the co‐parenting questionnaire has satisfactory psychometric properties with acceptable reliability and validity for measuring joint parenting among Iranian parents in terms of family integrity, consistency and conflict dimensions.
Centralised by Design: Anglocentric Constitutionalism, Accountability and the Failure of English Devolution
Authors: Denham John , Morphet Janice
Published: November 2024

The Labour manifesto in this year's election implied a radical restructuring of the UK state, the way in which England is governed and in relations across the United Kingdom. The aim of making English devolution the ‘default option’ is set against fifty years of unsuccessful and partial devolution initiatives which have failed to reverse the accretion of power in the central UK state. Centralisation can be seen as the consequence of an Anglocentric constitutionalism which vests power in the centre, underpins England's fragmented departmental governance and where accountability mechanisms flow to HM Treasury. Labour's success will reflect its willingness to challenge these constitutional assumptions, which are deeply embedded in the culture, practice and structures of Westminster and Whitehall. Successful devolution will require breaking the chains of accountability that tie local spending decisions to the centre and placing devolved English local government on a stronger constitutional basis.
AI in microbiome‐related healthcare
Authors: Probul Niklas , Huang Zihua , Saak Christina Caroline , Baumbach Jan , List Markus
Published: November 2024

Artificial intelligence (AI) has the potential to transform clinical practice and healthcare. Following impressive advancements in fields such as computer vision and medical imaging, AI is poised to drive changes in microbiome‐based healthcare while facing challenges specific to the field. This review describes the state‐of‐the‐art use of AI in microbiome‐related healthcare. It points out limitations across topics such as data handling, AI modelling and safeguarding patient privacy. Furthermore, we indicate how these current shortcomings could be overcome in the future and discuss the influence and opportunities of increasingly complex data on microbiome‐based healthcare.
Optimized psilocybin production in tryptophan catabolism‐repressed fungi
Authors: Janevska Slavica , Weiser Sophie , Huang Ying , Lin Jun , Hoefgen Sandra , Jojić Katarina , Barber Amelia E. , Schäfer Tim , Fricke Janis , Hoffmeister Dirk , Regestein Lars , Valiante Vito , Kufs Johann E.
Published: November 2024

The high therapeutic potential of psilocybin, a prodrug of the psychotropic psilocin, holds great promise for the treatment of mental disorders such as therapy‐refractory depression, alcohol use disorder and anorexia nervosa. Psilocybin has been designated a ‘Breakthrough Therapy’ by the US Food and Drug Administration, and therefore a sustainable production process must be established to meet future market demands. Here, we present the development of an in vivo psilocybin production chassis based on repression of l‐tryptophan catabolism. We demonstrate the proof of principle in Saccharomyces cerevisiae expressing the psilocybin biosynthetic genes. Deletion of the two aminotransferase genes ARO8/9 and the indoleamine 2,3‐dioxygenase gene BNA2 yielded a fivefold increase of psilocybin titre. We transferred this knowledge to the filamentous fungus Aspergillus nidulans and identified functional ARO8/9 orthologs involved in fungal l‐tryptophan catabolism by genome mining and cross‐complementation. The double deletion mutant of A. nidulans resulted in a 10‐fold increased psilocybin production. Process optimization based on respiratory activity measurements led to a final psilocybin titre of 267 mg/L in batch cultures with a space–time‐yield of 3.7 mg/L/h. These results demonstrate the suitability of our engineered A. nidulans to serve as a production strain for psilocybin and other tryptamine‐derived pharmaceuticals.
Unlocking the potential for microbiome‐based therapeutics to address the sustainable development goal of good health and wellbeing
Authors: Gulliver Emily L. , Di Simone Sara K. , Chonwerawong Michelle , Forster Samuel C.
Published: November 2024

Recent years have witnessed major advances and an ever‐growing list of healthcare applications for microbiome‐based therapeutics. However, these advances have disproportionately targeted diseases common in high‐income countries (HICs). Within low‐ to middle‐income countries (LMIC), opportunities for microbiome‐based therapeutics include sexual health epidemics, maternal health, early life mortality, malnutrition, vaccine response and infectious diseases. In this review we detail the advances that have been achieved in microbiome‐based therapeutics for these areas of healthcare and identify where further work is required. Current efforts to characterise microbiomes from LMICs will aid in targeting and optimisation of therapeutics and preventative strategies specifically suited to the unmet needs within these populations. Once achieved, opportunities from disease treatment and improved treatment efficacy through to disease prevention and vector control can be effectively addressed using probiotics and live biotherapeutics. Together these strategies have the potential to increase individual health, overcome logistical challenges and reduce overall medical, individual, societal and economic costs.
Proton motive force and antibiotic tolerance in bacteria
Authors: Wan Yingkun , Zheng Jiaqi , Chan Edward Wai‐Chi , Chen Sheng
Published: November 2024

Bacterial antibiotic tolerance is a decades‐old phenomenon in which a bacterial sub‐population, commonly known as persisters, does not respond to antibiotics and remains viable upon prolonged antimicrobial treatment. Persisters are detectable in populations of bacterial strains that are not antibiotic‐resistant and are known to be responsible for treatment failure and the occurrence of chronic and recurrent infection. The clinical significance of antibiotic tolerance is increasingly being recognized and comparable to antibiotic resistance. To eradicate persisters, it is necessary to understand the cellular mechanisms underlying tolerance development. Previous works showed that bacterial antibiotic tolerance was attributed to the reduction in metabolic activities and activation of the stringent response, SOS response and the toxin–antitoxin system which down‐regulates transcription functions. The latest research findings, however, showed that decreased metabolic activities alone do not confer a long‐lasting tolerance phenotype in persisters, and that active defence mechanisms such as efflux and DNA repair are required for the long‐term maintenance of phenotypic tolerance. As such active tolerance‐maintenance mechanisms are energy‐demanding, persisters need to generate and maintain the transmembrane proton motive force (PMF) for oxidative phosphorylation. This minireview summarizes the current understanding of cellular mechanisms essential for prolonged expression of phenotypic antibiotic tolerance in bacteria, with an emphasis on the importance of generation and maintenance of PMF in enabling proper functioning of the active tolerance mechanisms in persisters. How such mechanisms can be utilized as targets for the development of anti‐persister strategies will be discussed.
Impaired suppression of fatty acid release by insulin is a strong predictor of reduced whole‐body insulin‐mediated glucose uptake and skeletal muscle insulin receptor activation
Authors: Schleh Michael W. , Ryan Benjamin J. , Ahn Cheehoon , Ludzki Alison C. , Van Pelt Douglas W. , Pitchford Lisa M. , Chugh Olivia K. , Luker Austin T. , Luker Kathryn E. , Samovski Dmitri , Abumrad Nada A. , Burant Charles F. , Horowitz Jeffrey F.
Published: November 2024

Aim

To examine factors underlying why most, but not all, adults with obesity exhibit impaired insulin‐mediated glucose uptake, we compared: (1) adipose tissue fatty acid (FA) release, (2) skeletal muscle lipid droplet (LD) characteristics, and (3) insulin signalling events, in skeletal muscle of adults with obesity with relatively high versus low insulin‐mediated glucose uptake.

Methods

Seventeen adults with obesity (BMI: 36 ± 3 kg/m2) completed a 2 h hyperinsulinemic–euglycemic clamp with stable isotope tracer infusions to measure glucose rate of disappearance (glucose Rd) and FA rate of appearance (FA Ra). Skeletal muscle biopsies were collected at baseline and 30 min into the insulin infusion. Participants were stratified into HIGH (n = 7) and LOW (n = 10) insulin sensitivity cohorts by their glucose Rd during the hyperinsulinemic clamp (LOW< 400; HIGH >550 nmol/kgFFM/min/[μU/mL]).

Results

Insulin‐mediated suppression of FA Ra was lower in LOW compared with HIGH (p < 0.01). In skeletal muscle, total intramyocellular lipid content did not differ between cohorts. However, the size of LDs in the subsarcolemmal region (SS) of type II muscle fibres was larger in LOW compared with HIGH (p = 0.01). Additionally, insulin receptor‐β (IRβ) interactions with regulatory proteins CD36 and Fyn were lower in LOW versus HIGH (p < 0.01), which aligned with attenuated insulin‐mediated Tyr phosphorylation of IRβ and downstream insulin‐signalling proteins in LOW.

Conclusion

Collectively, reduced ability for insulin to suppress FA mobilization, with accompanying modifications in intramyocellular LD size and distribution, and diminished IRβ interaction with key regulatory proteins may be key contributors to impaired insulin‐mediated glucose uptake commonly found in adults with obesity.