bluuebunny/crossref_metadata_2025_split huggingface dataset:
A temporal map of division, chromatin modification, and identity specification in the regenerating root
Authors: Rahni Ramin , Guillotin Bruno , Lee Laura R. , Birnbaum Kenneth D. 
Published: January 2024

AbstractPlants have a remarkable capacity for regeneration. InArabidopsis thaliana(Arabidopsis), the entire root tip—housing stem cells and specialized cells like the gravity-sensing columella—can be cut off and the remnant tissue will rapidly divide and differentiate to replace these missing identities. Despite some knowledge of the molecular mechanisms driving this process, the necessity of cell division in this context is not fully understood. Here, we define a timeline of the major steps in regeneration and investigate the role of division and chromatin remodeling in that time. We show that while cell cycle inhibition blocks regeneration, some partial reprogramming can still occur. We outline three broad processes during regeneration—ectopic stem cell niche gene expression, loss of remnant identities, and gain of new identities—and show that some reprogramming events like ectopic stem cell niche gene expression are division-independent. We find that the cell cycle is also accelerated during root regeneration, speeding up to nearly three times faster than in uncut roots. Moreover, we show that histone deacetylase (HDAC) activity is critical at the very early stages of regeneration, potentially preceding the role of cell division. Intriguingly, a one-hour treatment with the HDAC inhibitor Trichostatin A (TSA) immediately upon root tip removal is sufficient to significantly perturb regeneration, whereas a one-hour cell cycle inhibition is not. We propose that Class I HDACs are the prime mediators of this HDAC inhibition and implicateHDA19as a potential regulator of early reprogramming in root tip regeneration.
An inappropriate decline in ribosome levels drives a diverse set of neurodevelopmental disorders
Authors: Ni Chunyang , Yu Leqian , Vona Barbara , Park Dayea , Wei Yulei , Schmitz Daniel A , Wei Yudong , Ding Yi , Sakurai Masahiro , Ballard Emily , Liu Yan , Kumar Ashwani , Xing Chao , Kim Hyung-Goo , Ekmekci Cumhur , Karimiani Ehsan Ghayoor , Imannezhad Shima , Eghbal Fatemeh , Badv Reza Shervin , Schwaibold Eva Maria Christina , Dehghani Mohammadreza , Mehrjardi Mohammad Yahya Vahidi , Metanat Zahra , Eslamiyeh Hosein , Khouj Ebtissal , Alhajj Saleh Mohammed Nasser , Chedrawi Aziza , Alves César Augusto Pinheiro Ferreira , Houlden Henry , Kruer Michael , Alkuraya Fowzan S. , Cenik Can , Maroofian Reza , Wu Jun , Buszczak Michael 
Published: January 2024

SummaryMany neurodevelopmental defects are linked to perturbations in genes involved in housekeeping functions, such as those encoding ribosome biogenesis factors. However, how reductions in ribosome biogenesis can result in tissue and developmental specific defects remains a mystery. Here we describe new allelic variants in the ribosome biogenesis factorAIRIMprimarily associated with neurodevelopmental disorders. Using human cerebral organoids in combination with proteomic analysis, single-cell transcriptome analysis across multiple developmental stages, and single organoid translatome analysis, we identify a previously unappreciated mechanism linking changes in ribosome levels and the timing of cell fate specification during early brain development. We find ribosome levels decrease during neuroepithelial differentiation, making differentiating cells particularly vulnerable to perturbations in ribosome biogenesis during this time. Reduced ribosome availability more profoundly impacts the translation of specific transcripts, disrupting both survival and cell fate commitment of transitioning neuroepithelia. Enhancing mTOR activity by both genetic and pharmacologic approaches ameliorates the growth and developmental defects associated with intellectual disability linked variants, identifying potential treatment options for specific brain ribosomopathies. This work reveals the cellular and molecular origins of protein synthesis defect-related disorders of human brain development.HighlightsAIRIMvariants reduce ribosome levels specifically in neural progenitor cells.Inappropriately low ribosome levels cause a transient delay in radial glia fate commitment.Reduced ribosome levels impair translation of a selected subset of mRNAs.Genetic and pharmacologic activation of mTORC1 suppresses AIRIM-linked phenotypes.
p110α-dependent hepatocyte signaling is critical for liver gene expression and its rewiring in MASLD
Authors: Régnier Marion , Polizzi Arnaud , Fougeray Tiffany , Fougerat Anne , Perrier Prunelle , Anderson Karen , Lippi Yannick , Sarra Smati , Lukowicz Céline , Lasserre Frédéric , Fouche Edwin , Huillet Marine , Rives Clémence , Tramunt Blandine , Naylies Claire , Garcia Géraldine , Rousseau-Bacquié Elodie , Bertrand-Michel Justine , Canlet Cécile , Chevolleau-Mege Sylvie , Debrauwer Laurent , Heymes Christophe , Burcelin Rémy , Levade Thierry , Gourdy Pierre , Wahli Walter , Blum Yuna , Gamet-Payrastre Laurence , Ellero-Simatos Sandrine , Guillermet-Guibert Julie , Hawkins Phillip , Stephens Len , Postic Catherine , Montagner Alexandra , Loiseau Nicolas , Guillou Hervé 
Published: January 2024

AbstractInsulin and other growth factors are key regulators of liver gene expression, including in metabolic diseases. Most of the phosphoinositide 3-kinase (PI3K) activity induced by insulin is dependent on PI3Kα. We used mice lacking p110α, the catalytic subunit of PI3Kα, to investigate its role in the regulation of liver gene expression in health and in Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD). The absence of hepatocyte PI3Kα signaling promoted glucose intolerance in lean mice and significantly regulated liver gene expression, including insulin-sensitive genes, inad libitumfeeding. Some of the defective regulation of gene expression in response to hepatocyte-restricted insulin receptor deletion was related to PI3Kα signaling. In addition, though PI3Kα deletion in hepatocytes promoted insulin resistance, it was protective against steatotic liver disease in diet-induced obesity. In the absence of hepatocyte PI3Kα, the effect of diet-induced obesity on liver gene expression was significantly altered, with changes in rhythmic gene expression in liver. Altogether, this study highlights the specific role of p110α in the control of liver gene expression in physiology and in the metabolic rewiring that occurs during MASLD.
Maternal den site fidelity of polar bears in western Hudson Bay
Authors: Klappstein Natasha , McGeachy David , Pilfold Nicholas , Lunn Nicholas , Derocher Andrew 
Published: January 2024

AbstractSeasonal migrations allow to access temporally varying resources and individuals may show fidelity to specific locations. Polar bears (Ursus maritimus) are a sea ice dependent species that migrate between marine and terrestrial habitats, the latter being important for parturition and early cub rearing. However, fidelity to maternity den sites is poorly understood. We assessed polar bear maternal den site fidelity of the Western Hudson Bay subpopulation in Manitoba, Canada. Using capture and telemetry data collected between 1979−2018, we examined site fidelity from 188 maternity den locations from 78 individuals. We calculated within-individual inter-year distances between dens, and compared these to between-individual distances via non-parametric bootstrapping. We used generalised additive models to assess how maternal age, years between denning events, and sea ice conditions affected site fidelity. We found some evidence of site fidelity, as within-individual inter-year distances were smaller than between-individual den distances by approximately 18.5 km. As time between captures increased, inter-den distances also increased (ranging from approximately 25 km to 55 km), but no other variables significantly affected fidelity. Our findings suggest that western Hudson Bay polar bears show a moderate amount of fidelity to denning areas, but not necessarily to specific sites.
Arthropod community composition in urban landscapes is shaped by both environmental filtering and dispersal limitation
Authors: Roper-Edwards Indigo R. , Hurlbert Allen H. 
Published: January 2024

AbstractWe assessed the relative importance of environmental filtering and dispersal limitation in structuring foliage- and ground-dwelling arthropod communities in central North Carolina. We hypothesized that both the local environment and the dispersal distance between sites would predict community composition, but that dispersal distance would be more important for ground arthropods than for foliage arthropods. In both groups, variation in habitat characteristics was important in structuring communities, and the role of dispersal in structuring communities was much greater after accounting for variation in landscape connectivity. Our results demonstrate the importance of both dispersal limitation and environmental filtering in shaping community composition and emphasize the importance of variation in the landscape for modeling these forces. Examining communities of multiple arthropod groups across the same spatial gradient highlights the scale-dependence of these processes and illustrates how variation in the environment can alter the relative abundance of specialist and generalist taxa.
Feedback loop regulation between viperin and viral hemorrhagic septicemia virus through competing protein degradation pathways
Authors: Lu Xiaobing , Yi Meisheng , Hu Zhe , Yang Taoran , Zhang Wanwan , Marsh E. Neil G. , Jia Kuntong 
Published: January 2024

AbstractViperin is an antiviral protein that exhibits a remarkably broad spectrum of antiviral activity. Viperin-like proteins are found all kingdoms of life, suggesting it is an ancient component of the innate immune system. However, viruses have developed strategies to counteract viperin’s effects. Here, we describe a feedback loop between viperin and viral hemorrhagic septicemia virus (VHSV), a common fish pathogen. We show thatLateolabrax japonicusviperin (Ljviperin) is induced by both IFN-independent and IFN-dependent pathways, with the C-terminal domain ofLjviperin being important for its anti-VHSV activity.Ljviperin exerts an antiviral effect by binding both the nucleoprotein (N) and phosphoprotein (P) of VHSV and induces their degradation through the autophagy pathway, which is an evolutionarily conserved antiviral mechanism. However, counteracting viperin’s activity, N protein targets and degrades transcription factors that up-regulateLjviperin expression, interferon regulatory factor (IRF) 1 and IRF9, through ubiquitin-proteasome pathway. Together, our results reveal a previously unknown feedback loop between viperin and virus, providing potential therapeutic targets for VHSV prevention.ImportanceViral hemorrhagic septicaemia (VHS) is a contagious disease caused by the viral hemorrhagic septicaemia virus (VHSV), which poses a threat to over 80 species of marine and freshwater fish. Currently, there are no effective treatments available for this disease. Understanding the mechanisms of VHSV-host interaction is crucial for preventing viral infections. Here, we found that, as an ancient antiviral protein, viperin degrades the N and P proteins of VHSV through the autophagy pathway. Additionally, the N protein also impacts the biological functions of IRF1 and IRF9 through the ubiquitin-proteasome pathway, leading to the suppression of viperin expression. Therefore, the N protein may serve as a potential virulence factor for the development of VHSV vaccines and screening of antiviral drugs. Our research will serve as a valuable reference for the development of strategies to prevent VHSV infections.
A bibliometric analysis of neurobiological and behavioral disturbances of cafeteria diet interventions
Authors: Lopez-Castro Alejandra 
Published: January 2024

AbstractObesity is a global epidemic mainly caused by the overconsumption of western diets, high in fat and sugars. Cafeteria diet administered to rodents is an effective model of the metabolic, neurobiological, and behavioral disturbances caused by the over consumption of western diet in humans. However, this is still an emerging research field. To provide information about the past, present and future of the research field, this study aims to explore the research field of cafeteria diet and behavior through bibliometric analysis. Original articles on cafeteria diet and behavior were obtained from Pubmed, Scopus and Web of Science databases from 2013 to Octuber 30, 2023. The R packages litsearchr, bibliometrix, sjrdata and mblm were used for descriptive and inferential statistics. Linear regression, concept mapping and trend analysis were used for relationship analysis. 85 articles included from 457 authors, 20 countries and 56 institutions were included. 46 from Pubmed, 12 from Scopus and 27 from Web of Science. The 25 topmost productive authors were from Spain, Brazil, Australia, Switzerland, and USA. 15 authors had an h-index higher than 3. The institution with the largest production of articles is the University of South Wales with 10 articles. A simple linear regression could not establish significance between the relationship between the impact factor and the number of citations received. In addition, a conceptual structure map was performed, and 5 clusters were found. Finally, by a bi-factor analysis, a trend topic established that anxiety is the term currently in trend and since 2017 in the cafeteria diet and behavior research field. The present study explores the performance of authors, countries, institutions, and journals on classical measures of scientific parameters. This helped to model multiple correspondence and trend analyses that provide a reliable source of information to direct research on cafeteria diet interventions.
Estrogen receptor-related receptor (Esrra) induces ribosomal protein Rplp1-mediated adaptive hepatic translation during prolonged starvation
Authors: Tripathi Madhulika , Gauthier Karine , Sandireddy Reddemma , Zhou Jin , Gupta Priyanka , Sakthivel Suganya , Jiemin Nah , Arul Kabilesh , Tikno Keziah , Park Sung-Hee , Wang Lijin , Ho Lena , Giguere Vincent , Ghosh Sujoy , McDonnell Donald P. , Yen Paul M. , Singh Brijesh K. 
Published: January 2024

AbstractProtein translation is an energy-intensive ribosome-driven process that is reduced during nutrient scarcity to conserve cellular resources. During prolonged starvation, cells selectively translate specific proteins to enhance their survival (adaptive translation); however, this process is poorly understood. Accordingly, we analyzed protein translation and mRNA transcription by multiple methodsin vitroandin vivoto investigate adaptive hepatic translation during starvation. While acute starvation suppressed protein translation in general, proteomic analysis showed that prolonged starvation selectively induced translation of lysosome and autolysosome proteins. Significantly, the expression of the orphan nuclear receptor, estrogen-related receptor alpha (Esrra) increased during prolonged starvation and served as a master regulator of this adaptive translation by transcriptionally stimulating 60S acidic ribosomal protein P1 (Rplp1) gene expression. Overexpression or siRNA knockdown of Esrra expressionin vitroorin vivoled to parallel changes in Rplp1 gene expression, lysosome/autophagy protein translation, and autophagy. Remarkably, we have found that Esrra had dual functions by not only regulating transcription but also controling adaptive translation via the Esrra/Rplp1/lysosome/autophagy pathway during prolonged starvation.
Towards a phylogenomic classification of Magnoliidae
Authors: Helmstetter Andrew J. , Ezedin Zacky , de Lírio Elton John , de Oliveira Sylvia M. , Chatrou Lars W. , Erkens Roy H.J. , Larridon Isabel , Leempoel Kevin , Maurin Olivier , Roy Shyamali , Zuntini Alexandre R. , Baker William J. , Couvreur Thomas L.P. , Forest Félix , Sauquet Hervé 
Published: January 2024

ABSTRACTPremiseMagnoliidae are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses of a limited number of mostly plastid markers have led to the current classification of magnoliids into four orders and 18 families. However, uncertainty remains regarding the placement of several families.MethodsHere we present the first comprehensive phylogenomic analysis of Magnoliidae as a whole, sampling 235 species from 199 (74%) genera and representing all families and most previously accepted subfamilies and tribes. We analyze newly generated data from the Angiosperms353 probe set using both coalescent and concatenation analyses and testing the impact of multiple filtering and alignment strategies.ResultsWhile our results generally provide further support for previously established phylogenetic relationships in both magnoliids as a whole and large families including Annonaceae and Lauraceae, they also provide new evidence for previously ambiguous relationships. In particular, we find support for the position of Hydnoraceae as sister to the remainder of Piperales and, for the first time, resolve the backbone of relationships among most genera of Myristicaceae.ConclusionsAlthough some of our results are limited by low gene recovery for a number of taxa and significant gene tree conflict for some relationships, this study represents a significant step towards reconstructing the evolutionary history of a major lineage of angiosperms. Based on these results, we present an updated phylogenetic classification for Magnoliidae, recognizing 21 families, summarizing previously established subfamilies and tribes, and describing new tribes for Myristicaceae.
Analysis of 193,618 trauma patient presentations in war-affected Syria from July 2013 to July 2015
Authors: Mowafi Hani , Hariri Mahmoud , Zhang Baobao , Alnahhas Houssam , Bakri Basil , Eldahan Adam , Moustafa Moustafa , Saqqur Maher , Al-Kassem Anas 
Published: January 2024

AbstractIntroductionSince 2011, the Syrian war has produced a mounting toll in terms of deaths and displaced persons. We present an analysis of demographic and temporal patterns of trauma patient presentations to Syrian hospitals in non-governmental, non-Islamic State (NGNI) regions from 2013 – 2015.MethodsWe analyzed an administrative dataset of patient presentations to 95 NGNI Syrian hospitals in regions outside of Syrian government control from July 2013 – July 2015. Descriptive analysis of this secondary data is reported and logistic regression was performed to assess for factors associated with inpatient mortality.Results193,618 trauma patients presented to 95 NGNI hospitals from July 2013 – July 2015 (154,225 male, 79.7%; 39,393 female, 20.4%). Age information was complete for 160,237 encounters (82.8%): 0-2y: 8,257 (4.3%), 3-12y: 24,199 (12.5%), 13-18y: 22,482 (11.6%), 19-60y: 100,553 (51.9%), and elders over 60 years: 4,746 (2.5%). 59,387 patients were admitted (Ward 57,625; ICU 1,762) for an average length of stay of 3.80 days. There were 2,694 inpatient deaths (4.5% of admitted) and 4,758 patients (8.0%) required transfer to another facility for definitive care. Shrapnel (81,946; 42.3%) and blunt/crush injuries (71,477; 36.9%) were dominant injury mechanisms with an increasing proportion of these injuries over time. Inpatient mortality was most associated with extremes of age (age less than 2 aOR 2.92; age greater than 60 aOR 2.48), penetrating chest trauma (gunshot-chest aOR 6.03) and neurotrauma (blast-head aOR 13.42; blast-spine aOR 11.31; gunshot-head aOR 10.07; shrapnel-head aOR 6.34). Civilians presentations increased from 20% at start of data collection to a peak of 50% in June 2015.ConclusionThe Syrian war has resulted in large volumes of trauma patients and significant mortality at NGNI Syrian hospitals. Mortality was most associated with neurotrauma and penetrating chest trauma. There was an increasing trend over time towards blunt/crush and shrapnel injuries consistent with the transition to the widespread use of aerial bombardment with resultant explosions and building collapse. Civilians including children and the elderly represent high proportions of the injured in NGNI Syrian hospitals. Additional work is needed to improve documentation of clinical service and to assess outcomes of care to improve quality of services provided to Syrian war trauma patients.
Discovery and validation of plasma-based protein biomarkers for the aetiological distinction of bacterial and non-bacterial febrile infections in African children
Authors: Waeni Jacqueline M , Chege Timothy K , Gicheru Elijah T , Mutunga Martin , Njunge James , O’Connor Daniel , Sande Charles J 
Published: January 2024

AbstractBackgroundIn many low resource settings, the clinical management of children with febrile infections is hindered by poor access to diagnostic tools to determine whether the cause of an infection is bacterial, viral or parasitic. As a result, many clinicians resort to the default prescription of antibiotics as a safety precaution, contributing to the alarming spread of antimicrobial resistance. Commonly used biomarkers for identification of bacterial sepsis such as CRP lack aetiological specificity and are frequently elevated by non-bacterial infections including malaria. We set out to discover and validate new biomarkers for the characterization of the microbial aetiology of febrile acute infections in Kenyan children.MethodsWe recruited a discovery cohort comprising of children who had been admitted to hospital with a variety of severe acute infections. Diagnostic identification of viral infections was done using a 15-target virus PCR panel, bacterial infections were identified using blood culture while malaria infections were identified by microscopy. Using mass spectrometry analysis, we identified a set of 76 plasma proteins whose abundance varied significantly by the microbial aetiology of infection and used machine learning to generate a shortlist of candidate biomarkers that had the highest diagnostic performance in distinguishing aetiologies. To validate these candidate biomarkers, we recruited a separate validation cohort where the plasma levels of the shortlisted biomarkers were assayed among children with different infectious aetiologies using a custom protein microarray.ResultsIn the discovery study, six candidate biomarkers whose plasma abundance was significantly different in children with bacterial and viral infections were shortlisted by random forest for cross-cohort validation (AGT, HRG, LBP, PON1, SERPINA1, SERPINA3). In the validation study, we found that of the six biomarkers, only AGT compared favourably to CRP and identified febrile bacterial infections with a sensitivity of 72.4% (95% CI 48.4% - 83.6%) compared to CRP which distinguished febrile bacterial infections with a sensitivity of 69.5% (30.8% - 88.2%). Plasma AGT was superior to CRP in distinguishing children with febrile bacterial infections from those with febrile malaria episodes, with a sensitivity of 72.5% (40% - 84.6%) for AGT and 26% (15% - 32.8%) for CRP.ConclusionsWe report the discovery of AGT, as a sensitive plasma biomarker for the identification of febrile bacterial infections among African children living in a malaria endemic setting.