bluuebunny/crossref_metadata_2025_split huggingface dataset:
ERECTA family signaling controls cell fate specification during ovule initiation in Arabidopsis
Authors: Overholt Alex M. , Pierce Christina Elaine , Paleologos Calen Seth , Shpak Elena D. 
Published: October 2024

AbstractThe number of seeds produced by a plant depends on the number of ovules initiated within the carpels by a meristematic tissue, the placenta. Previous studies indicated that ERECTA-LIKE1 (ERL1) and ERL2 receptors and their extracellular ligand EPIDERMAL PATTERNING FACTOR-LIKE2 (EPFL2) promote seed density while ERECTA inhibits it. Here, we show that all three receptors and two ligands, EPFL1 and EPFL2, promote ovule initiation. After initiation, EPFL1 and EPFL2 redundantly regulate the elongation of nascent ovules and promote the growth of the funiculus. The synergy of EPFL1 and EPFL2 withCUP-SHAPED COTYLEDONboundary genes in the regulation of ovule number and shape suggests cooperation in their function. Ovule initiation starts with the specification of ovule founder cells that are separated by boundary cells. During ovule bulging, a new cell type, characterized by a high proliferative rate, forms between ovule founder and boundary cells. In theepfl1 epfl2mutant, marker genes for ovule founder and boundary cells are expressed much more broadly. Our data indicate that ERECTA family signaling is necessary for efficient cell fate separation at the earliest stages of ovule initiation. Later, it promotes the formation of a zone of high proliferation at the base of the ovule.
Obesity-Associated Changes in Immune Cell Dynamics During Alphavirus Infection Revealed by Single Cell Transcriptomic Analysis
Authors: Hameed Muddassar , Daamen Andrea R. , Hossain Md Shakhawat , Coutermarsh-Ott Sheryl , Lipsky Peter E. , Weger-Lucarelli James 
Published: October 2024

SummaryObesity induces diverse changes in host immunity, resulting in worse disease outcomes following infection with various pathogens, including arthritogenic alphaviruses. However, the impact of obesity on the functional landscape of immune cells during arthritogenic alphavirus infection remains unexplored. Here, we used single-cell RNA sequencing (scRNA-seq) to dissect the blood and tissue immune responses to Mayaro virus (MAYV) infection in lean and obese mice. Footpad injection of MAYV caused significant shifts in immune cell populations and induced robust expression of interferon response and proinflammatory cytokine genes and related pathways in both blood and tissue. In MAYV-infected lean mice, analysis of the local tissue response revealed a unique macrophage subset with high expression of IFN response genes that was not found in obese mice. This was associated with less severe inflammation in lean mice. These results provide evidence for a unique macrophage population that may contribute to the superior capacity of lean mice to control arthritogenic alphavirus infection.Graphical abstractHighlightsObesity worsens disease outcomes following arthritogenic alphavirus infection.Arthritogenic alphavirus infection causes significant shifts in immune cell populations in the blood and footpad.Blood monocytes from lean mice had higher expression of interferon response genes at the later stage of infection.Footpads in lean mice have an expanded population of F4/80lo macrophages with an intense interferon response gene signature before and after alphavirus infection that is not found in obese mice.Macrophages in obese mice express lower levels of interferon response genes, have a unique necroptosis signature, and higher F4/80 expression.
The polyketide pathway in sporopollenin biosynthesis is specific to land plants (Embryophyta)
Authors: Sraan Damanpreet K. , Ashton Neil W. , Suh Dae-Yeon 
Published: October 2024

AbstractBackground and AimsSporopollenin (SP) is a complex biopolymer in the outer wall of spores and pollen and provides protection from environmental stresses. Its extraordinary chemical resistance, especially to acetolysis, was widely used to identify SP in biological specimens. This broad definition of SP led to claims for its widespread occurrence among diverse embryophyte and non-embryophyte taxa. We previously proposed a biochemical definition that can be used to distinguish genuine SP from other chemically resistant cell wall materials. The definition was centred on ASCL (Anther-Specific Chalcone synthase-Like), an embryophyte-specific enzyme of the polyketide pathway that provides precursors for SP biosynthesis. Herein, we examine the evolution and distribution of all five enzymes (CYP703A, CYP704B, ACOS, ASCL and TKPR) of the polyketide pathway and propose a new, more comprehensive definition of SP.MethodsWe performed BLASTp searches, phylogenetic tree construction, protein modeling and sequence analysis to determine the presence or absence of ACOS and TKPR in embryophytes and streptophytic algae.Key ResultsWe found evidence that all five enzymes of the polyketide pathway evolved from ancestral enzymes of primary metabolism and ACOS, ASCL and TKPR were co-selected during evolution. The dosage of all five genes has been subjected to strict evolutionary control and, in some taxa, synteny has provided a selective advantage. All five enzymes are present in embryophytes but absent in green algae, indicating that the polyketide pathway and therefore SP is embryophyte-specific.ConclusionsThe addition of the polyketide pathway in the definition of genuine SP will allow separation of SP from algaenans and other chemically resistant ‘SP-like’ algal spore wall substances. This study further signifies SP as an evolutionary innovation unique to the embryophyte lineage and encourages research on possible evolutionary relationship between algal spore wall ‘SP-like materials’ and embryophyte SP.
Fentanyl reinforcement history has sex-specific effects on multi-step decision-making
Authors: Garr Eric , Cheng Yifeng , Castell Laia , Dong Andy , Shuai Cecelia , Wang Yunru , Min Jennifer , Camhi Zachary , Nay Albert , Malloy Nora , Janak Patricia H. 
Published: October 2024

ABSTRACTIt is commonly thought that drug addiction involves a transition to habitual control of action, where the choice to consume drugs becomes automatized and reflects a failure to deliberate over possible negative outcomes. Determining whether the pursuit of addictive drugs is habitual is hampered by a lack of behavior assessments suitable for use during a bout of drug seeking. Therefore, to understand how variable histories of drug reinforcement might affect goal-directed and habitual pursuit of drug rewards, we trained rats to perform a multi-step decision-making task to earn oral fentanyl or sucrose rewards following extensive training with either fentanyl or sucrose. Importantly, this task allowed for independent measurements of goal-directed and habitual choice characteristics during online pursuit of rewards, and habitual choice could further be categorized into perseverative and reward-guided components. Extensive fentanyl training led to a bias for reward-guided habitual choice specifically in females, and a relatively high degree of perseveration in both sexes. These behavioral changes after chronic fentanyl generalized across fentanyl and sucrose seeking. In contrast, during fentanyl sessions, females showed increased perseveration, and both sexes showed blunting of the gradual improvement in goal-directed choice. These results show that chronic drug reinforcement induced habits that generalized across seeking drug and non-drug rewards, and female rats were especially susceptible to habitual control induced by both chronic and acute drug reinforcement.
Quantifying relative sponginess: a high-resolution model of landscape water retention as an ecosystem service
Authors: Evans Paul M. , Dussaillant Alejandro , Varma Varun , Redhead John W. , Pywell Richard F. , Storkey Jonathan , Mead Andrew , Bullock James M. 
Published: October 2024

AbstractUnprecedented climate and land use changes are having major impacts on water-based ecosystem services (ES). It is crucial, therefore, to get an in-depth understanding of current levels of such ES provision, and how they could be impacted by changed environments or management. However, applying existing models for water-related ES pose substantial challenges, which include the need for in-depth specialist hydrological knowledge, the requirement for numerous datasets and parameters that may not be consistently available, and high computational costs. Additionally, there is often a mismatch between the resolution of the model output and parcel-level land management, at which ES information is often most valuable for supporting decision-making.Here we detail a rapid method for assessing water retention potential by estimating an area’s ‘sponginess’ - its capacity to absorb and retain precipitation. Our approach builds upon a topography-adjusted Curve Number methodology, a widely recognised and straightforward tool for estimating water run-off. We calculated run-off across 1 km grid cells (representing field- to farm-scale land parcels) in Great Britain based on the land’s sponginess under storm conditions. The primary objective was to investigate the applicability of the method in estimating point-values — i.e., the independent contribution of each grid square — within the context of known limitations. The results enable the identification of areas with higher potential for the ES of water retention.Our model output illustrates the spectrum of sponginess across Great Britain, ranging from less than 30% of precipitation retained in city regions to as high as 99% in some rural, agricultural areas. Importantly, we demonstrate that the model is easy to run, can be used with freely-available data, and produces outputs compatible with grid-based models for other ES. Overall, the model provides an accessible approach to estimating the ES of water retention to researchers worldwide, even in data-scarce areas.Highlights-To inform land management decisions it is important to determine parcel-level ecosystem services, but there is a gap for services related to water.-Parcel-level assessments of a land’s ‘sponginess’ – the capacity to retain precipitation – are described.-Values are calculated using a topography-adjusted Curve Number methodology, which requires little data input or hydrological expertise.-‘Sponginess’ and run-off estimates are provided for Great Britain at 1 km resolution.
Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics
Authors: Du Heng , Zhuo Yue , Lu Shiyu , Li Wanying , Zhou Lei , Sun Feizhou , Liu Gang , Liu Jian-Feng 
Published: October 2024

AbstractPigs are among the most essential sources of high-quality protein in human diets. Structural variants (SVs) are a major source of genetic variants associated with diverse traits and evolutionary events. However, the current linear reference genome of pigs limits the presentation of position information for SVs. In this study, we generated a pangenome of pigs and a genome variation map of 599 deep-sequenced genomes across Eurasia. Moreover, a section-wide gene repertoire was constructed, which indicated that core genes were more evolutionarily conserved than variable genes. Subsequently, we identified 546,137 SVs, their enrichment regions, and relationships with genomic features and found significant divergence across Eurasian pigs. More importantly, the pangenome-detected SVs could complement heritability estimates and genome-wide association studies based only on single nucleotide polymorphisms. Among the SVs shaped by selection, we identified an insertion in the promoter region of theTBX19gene, which may be related to the development, growth, and timidity traits of Asian pigs and may affect the gene expression. Our constructed pig pangenome and the identified SVs provide rich resources for future functional genomic research on pigs.
Evaluating Sequence and Structural Similarity Metrics for Predicting Shared Paralog Functions
Authors: Dennler Olivier , Ryan Colm J. 
Published: October 2024

ABSTRACTGene duplication is the primary source of new genes, resulting in most genes having identifiable paralogs. Over evolutionary time scales, paralog pairs may diverge in some respects but many retain the ability to perform the same functional role. Protein sequence identity is often used as a proxy for functional similarity and can predict shared functions between paralogs as revealed by synthetic lethal experiments. However, the advent of alternative protein representations, including embeddings from protein language models (PLMs) and predicted structures from AlphaFold, raises the possibility that alternative similarity metrics could better capture functional similarity between paralogs. Here, using two species (budding yeast and human) and two different definitions of shared functionality (shared protein-protein interactions, synthetic lethality) we evaluated a variety of alternative similarity metrics. For some tasks, predicted structural similarity or PLM embedding similarity outperform sequence identity, but more importantly these similarity metrics are not redundant with sequence identity, i.e. combining them with sequence identity leads to improved predictions of shared functionality. By adding contextual features, representing similarity to homologous proteins within and across species, we can significantly enhance our predictions of shared paralog functionality. Overall, our results suggest that alternative similarity metrics capture complementary aspects of functional similarity beyond sequence identity alone.GRAPHICAL ABSTRACT
FiNNpy 2.0: Fast MEG source reconstruction
Authors: Crompton David , Keerthi Prerana , Milosevic Luka , Scherer Maximilian 
Published: October 2024

AbstractHerein, we present the 2.0 update of FiNNpy, which expands the toolkit’s initial scope from the analysis of multi-site electrophysiological activity to track information propagation to include source reconstruction capability for MEG signals. Following the toolkit’s de- sign guidelines, the new functionality has been optimized towards minimal resource consumption, making source reconstruction much faster, especially when executed in a parallelized fashion.Furthermore, several quality-of-life aspects are introduced to support source reconstruction, such as grouping source-space activity into cortical areas, a cohesive documentation & in-code extensive literature references, and wrapping of previously terminal exclusive functions of FreeSurfer.
A global analysis of domestic military policies governing responses to public health emergencies
Authors: Hu Kuang Yu , Weets Ciara M. , Wilson Rory , Ljungqvist Gunnar V. , Katz Rebecca 
Published: October 2024

AbstractThroughout the COVID-19 pandemic, militaries around the world mobilized at an unprecedented scale to support domestic response efforts. This was consistent with the growing trend of asset mobilization for military operations other than war during public health emergencies. However, the global scale and vast breadth of civil-military cooperation during the pandemic invites new considerations regarding the authority and scope of domestic operations of militaries during public health emergencies. We have systematically analyzed domestic military deployment policies in each UN member state, focusing on the authority, execution and scope of military involvement pertaining to domestic public health emergencies.We analyzed legally enforceable policies, including Constitutions, defense ministry authorizations, and legal frameworks. We categorized how each country codified the deployment of military assets, who holds authority for deployment and the procedural mechanisms for deployments. Our findings revealed that of countries with active military forces, nearly all (170/171) have codified rules on domestic military deployment and 90.59% (154/170) allow military mobilization through executive orders. Furthermore, 58.48% (100/171) of countries with an active military have codified separation of powers to ensure that civilian decision makers are exclusively empowered to mobilize military forces. Finally, we found that 74.85% (128/171) of countries included language that authorized military involvement in domestic military operations other than war.Our findings provide critical data for analyzing the relationship between military operations and public health outcomes, including how specific domestic military deployment policies impact the speed and effectiveness of military involvement in public health emergencies.
The associations between Screen Time, Screen Content, and ADHD risk based on the evidence of 41494 children from Longhua district, Shenzhen, China
Authors: Wu Jian-Bo , Yang Yanni , Zhou Qiang , Li Jiemin , Yang Wei-Kang , Yin Xiaona , Qiu Shuang-Yan , Zhang Jingyu , Meng Minghui , Chen Jian-hui , Chen Zhaodi 
Published: October 2024

ABSTRACTObjectiveThis study investigates the relationship between screen time, screen content, and the risk of Attention Deficit Hyperactivity Disorder (ADHD) using data from a large sample. Specifically, it examines how different types of screen content (such as educational videos, cartoon videos, and interactive videos) are associated with the risk of ADHD. The aim is to offer a scientific foundation for the rational management of children’s screen time and screen content.MethodsWe collected data through a questionnaire survey involving a study population of 41,494 children from Longhua District, Shenzhen City, China. The questionnaire recorded the daily screen time and the type of content viewed by the children at ages 1-3 years and assessed their risk of ADHD using the Strengths and Difficulties Questionnaire (SDQ) at ages 4-6 years. Hierarchical logistic regression analysis, controlling for confounding factors, was employed to explore the associations between screen time, screen content, and ADHD risk.ResultsIn the total sample, 6.7% of the participants had screen time exceeding 60 minutes per day, with educational videos predominant type (63.4%). 16.5% of the participants were identified as being at risk for ADHD. Statistically significant positive associations with ADHD were observed across all categories of screen time (P<0.001). Moreover, as screen time increased, the risk of ADHD also rose (OR1∼60 mins/d=1.627,95%CI=1.460∼1.813;OR61∼120 mins/d=2.838,95%CI=2.469∼3.261;OR>120 mins/d=3.687,95%CI=2.835∼4.796).Significant positive associations with ADHD were observed across all categories of screen time in the educational videos and cartoon videos. For the educational videos group, the odds ratios were as follows:OR1-60 mins/day=1.683 (95% CI=1.481-1.913),OR61-120 mins/day=3.193 (95% CI=2.658-3.835), andOR>120 mins/day=3.070 (95% CI=2.017-4.673). For the cartoon videos group, the odds ratios were:OR1-60 mins/day=1.603 (95% CI=1.290-1.991),OR61-120 mins/day=2.758 (95% CI=2.156-3.529), andOR>120 mins/day=4.097 (95% CI=2.760-6.081).However, no significant associations with ADHD risk were found for any category of screen time in the interactive videos group (OR1∼60 mins/d=0.744,95%CI=0.361∼1.534;OR61∼120 mins/d=0.680,95%CI=0.296∼1.560;OR>120 mins/d=1.678,95%CI=0.593∼4.748).ConclusionAs screen time increases, the risk of ADHD also rises. Both educational videos and cartoon videos show a positive correlation between screen time and ADHD risk. However, no significant association was found between screen time and ADHD risk when it came to interactive videos. This study underscores the importance of reasonably managing children’s screen time, particularly the time spent watching educational and cartoon videos.
CONTROL OFOROBANCHE CUMANAWALLR: RESEARCH ON SUSTAINABILITY OF SUNFLOWER HYBRIDS AND STRATEGIES FOR PARASITE PROTECTION
Authors: Khablak Serhii , Bondareva Lesia , Dolia Mykola , Blume Yaroslav , Tymoshchuk Tetiana , Mrynskyi Ivan , Hrytsiuk Natalia , Spychak Valentyn 
Published: October 2024

ABSTRACTThe work is devoted to solving an important scientific task of determining the spread and harmfulness of broomrape, its racial composition, and developing measures to protect sunflower from this parasite. The aim of the research was to determine the resistance of sunflower hybrids to the broomrape parasite. During the research, a vegetation experiment was used to determine the racial composition of the parasite and the resistance of different sunflower hybrids to it. Sunflower hybrids were evaluated for resistance to broomrape in soil culture using a modified method and the roll method of seed germination. From the northern Steppe of Ukraine, broomrape is actively moving to the central, northern and western regions of the country. The practical value of the work is to determine the resistance of sunflower hybrids to broomrape. Differentiation of sunflower hybrids grown by resistance to the parasite was carried out. It has been observed that the broomrape population exhibits a significant level of virulence capable of overcoming the immunity found in the most resilient foreign-bred hybrids resistant to E, F, and G races of this parasite. The appearance of highly aggressive new races of broomrape (E, F, G, and H) in the Forest-Steppe and Polissya regions underscores the crucial necessity to address the challenge of developing breeding material resistant to these novel races of the parasitic plant. This entails an in-depth exploration of the cellular and molecular mechanisms underlying sunflower resistance to the pathogen. The widespread buildup of parasite races E, F, G, and H in sunflower crops is linked to the disruption of crop rotations and the extensive cultivation of hybrids of this crop. These hybrids are primarily resistant to races 5 (E) and 6 (F) of the parasite.The results of the research can be used in the region’s farms for successful protection against broomrape, as well as in breeding programs to create sunflower hybrids resistant to new races of the parasite and corn hybrids that cause better germination of seeds of this pathogen in the soil and their death by their root secretions.
Appraisal of the causal effect ofChlamydia trachomatisinfection on epithelial ovarian cancer risk: a two-sample Mendelian randomisation study
Authors: Perrott Sarah L. , Kar Siddhartha P. 
Published: October 2024

AbstractBackgroundHistory ofChlamydia trachomatisinfection has previously been associated with epithelial ovarian cancer (EOC) in observational studies. We conducted a two-sample univariable Mendelian randomisation (MR) study to examine whether genetically predicted seropositivity to theC. trachomatismajor outer membrane protein (momp) D is causally associated with EOC.MethodsMR analyses employed genetic associations derived from UK Biobank as proxies for momp D seropositivity in 25 509 EOC cases and 40 941 controls that participated in the Ovarian Cancer Association Consortium. Findings were replicated using a GWAS meta-analyses of global biobanks including the UK Biobank, FinnGen and BioBank Japan.ResultsGenetically predicted momp D seropositivity was associated with overall and high-grade serous EOC risk in inverse-variance weighted (IVW) and MR-Egger univariable MR analysis (odds ratio (OR) 1.06; 95% confidence interval (CI) 1.02—1.10, and OR 1.08; 95%CI 1.01—1.16, respectively). Replication yielded similar results for overall EOC (OR 1.11; 95%CI 1.01—1.22).ConclusionThis MR study supports a causative link betweenC. trachomatisinfection and overall and high-grade serous EOC.