bluuebunny/crossref_metadata_2025 huggingface dataset:
FieldDino: High-throughput physio-morphological phenotyping of stomatal characteristics for plant breeding research
Authors: Chaplin Edward , Coleman Guy , Merchant Andrew , Salter William
Published: October 2024

Stomatal anatomy and physiology define CO2availability for photosynthesis and regulate plant water use. Despite being key drivers of yield and dynamic responsiveness to abiotic stresses, conventional measurement techniques of stomatal traits are laborious and slow, limiting adoption in plant breeding. Advances in instrumentation and data analyses present an opportunity to screen stomatal traits at scales relevant to plant breeding. We present a high-throughput field-based phenotyping approach, FieldDino, for screening of stomatal physiology and anatomy. The method allows coupled measurements to be collected in <15 s and consists of: (1) stomatal conductance measurements using a handheld porometer; (2)in situcollection of epidermal images with a digital microscope, 3D-printed leaf clip and Python-based app; and (3) automated deep learning analysis of stomatal features. The YOLOv8-M model trained on images collected in the field achieved strong performance metrics with an mAP@0.5 of 97.1% for stomatal detection. Validation in large field trials of 200 wheat genotypes with two irrigation treatments captured wide diversity in stomatal traits. FieldDino enables stomatal data collection and analysis at unprecedented scales in the field. This will advance research on stomatal biology and accelerate the incorporation of stomatal traits into plant breeding programs for resilience to abiotic stress.

Highlight

Chaplin et al., have developed FieldDino which enables rapid, high-throughput phenotyping of stomatal traits, advancing plant breeding research by integrating streamlined in-field measurements with automated deep learning analysis.
A CXCR4 partial agonist improves immunotherapy by targeting polymorphonuclear myeloid-derived suppressor cells and cancer-driven granulopoiesis
Authors: Qian Jin , Ma Chenkai , Waterbury Quin T. , Zhi Xiaofei , Moon Christine S. , Tu Ruhong , Kobayashi Hiroki , Wu Feijing , Zheng Biyun , Zeng Yi , Zheng Hualong , Ochiai Yosuke , White Ruth A. , Harle David W. , LaBella Jonathan S. , Zamechek Leah B. , Hu Lucas ZhongMing , Moy Ryan H. , Han Arnold S. , Daugherty Bruce , Lederman Seth , Wang Timothy C.
Published: October 2024

Polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) are pathologically activated neutrophils that potently impair immunotherapy responses. The chemokine receptor CXCR4, a central regulator of hematopoiesis, represents an attractive PMN-MDSC target1. Here, we fused a secreted CXCR4 partial agonist TFF2 to mouse serum albumin (MSA) and demonstrated that TFF2-MSA peptide synergized with anti-PD-1 to induce tumor regression or eradication, inhibited distant metastases, and prolonged survival in multiple gastric cancer (GC) models. Using histidine decarboxylase (Hdc)-GFP transgenic mice to track PMN-MDSCin vivo, we found TFF2-MSA selectively reduced the immunosuppressive Hdc-GFP+CXCR4hitumor PMN-MDSCs while preserving proinflammatory neutrophils, thereby boosting CD8+T cell-mediated anti-tumor response together with anti-PD-1. Furthermore, TFF2-MSA systemically reduced PMN-MDSCs and bone marrow granulopoiesis. In contrast, CXCR4 antagonism plus anti-PD-1 failed to provide a similar therapeutic benefit. In GC patients, expanded PMN-MDSCs containing a prominent CXCR4+LOX-1+subset are inversely correlated with the TFF2 level and CD8+T cells in circulation. Collectively, our studies introduce a strategy of using CXCR4 partial agonism to restore anti-PD-1 sensitivity in GC by targeting PMN-MDSCs and granulopoiesis.
DeepAllo: Allosteric Site Prediction using Protein Language Model (pLM) with Multitask Learning
Authors: Khokhar Moaaz , Keskin Ozlem , Gursoy Attila
Published: October 2024

Allostery, the process by which binding at one site perturbs a distant site, is being rendered as a key focus in the field of drug development with its substantial impact on protein function. The identification of allosteric pockets (sites) is a challenging task and several techniques have been developed, including Machine Learning (ML) to predict allosteric pockets that utilize both static and pocket features. Our work, DeepAllo, is the first study that combines fine-tuned protein language model (pLM) with FPocket features and shows an increase in prediction performance of allosteric sites over previous studies. The pLM model was fine-tuned on Allosteric Dataset (ASD) in Multitask Learning (MTL) setting and was further used as a feature extractor to train XGBoost and AutoML models. The best model predicts allosteric pockets with 89.66% F1 score and 90.5% of allosteric pockets in the top 3 positions, outperforming previous results. A case study has been performed on proteins with known allosteric pockets, which shows the proof of our approach. Moreover, an effort was made to explain the pLM by visualizing its attention mechanism among allosteric and non-allosteric residues.
Identification of leaf rust resistance loci in hard winter wheat using genome-wide association mapping
Authors: Lakkakula Indira Priyadarshini , Kolmer James A , Sharma Rajat , St. Amand Paul , Bernardo Amy , Bai Guihua , Ibrahim Amir , Bowden Robert L. , Carver Brett F. , Boehm Jeffrey D. , Aoun Meriem
Published: October 2024

Leaf rust, caused byPuccinia triticina(Pt), is a serious constraint to wheat production. Developing resistant varieties is the best approach to managing this disease. Wheat leaf rust resistance (Lr) genes have been classified into either all-stage resistance (ASR) or adult-plant resistance (APR). The objectives of this study were to identify sources of leaf rust resistance in contemporary U.S. hard winter wheat (HWW) and to dissect the genetic basis underlying leaf rust resistance in HWW. A panel of 732 elite HWW genotypes was evaluated for response to U.S.Ptraces at the seedling stage and at the adult plant stage in leaf rust nurseries in Oklahoma, Texas, and Kansas. Further, the panel was genotyped using Multiplex Restriction Amplicon Sequencing (MRA-Seq) and DNA markers linked to the known ASR genesLr18,Lr19,Lr21,Lr24,Lr37, andLr42and APR genesLr34,Lr46,Lr67,Lr68,Lr77, andLr78. Single nucleotide polymorphism (SNP) markers derived from MRA-Seq, DNA markers linked to the knownLrgenes, and the phenotypic data were used for genome-wide association study (GWAS) to identify markers associated with leaf rust response. Gene postulation based on leaf rust reactions, DNA markers, and GWAS suggested the presence ofLr1,Lr2a,Lr10,Lr14a,Lr16,Lr18,Lr19,Lr21,Lr24,Lr26,Lr34,Lr37, Lr39,Lr42,Lr46,Lr68,Lr77, andLr78in the HWW panel. The GWAS identified 59 SNPs significantly associated with leaf rust response, of which 20 were likely associated with novel resistance loci and can be used to enhance wheat leaf rust resistance.
Visualization and quantification of spatiotemporal disease progression in Arabidopsis using a bioluminescence-based imaging system
Authors: Taks Nanne W. , Batstra Mathijs , Kortekaas Ronald , Stevens Floris D. , Pfeilmeier Sebastian , van den Burg Harrold A.
Published: October 2024

Plant pathogenic bacteria use various entry strategies to colonize their host, like entering through natural openings and wounds in leaves and roots. The vascular pathogenXanthomonas campestrispv. campestris (Xcc) enters through hydathodes, organs at the leaf margin involved in guttation. Subsequently, Xcc breaks out from infected hydathodes, progressing into the xylem vessels and causing systemic disease. To elucidate the mechanisms that underpin the different stages of Xcc pathogenesis, a need exists to image Xcc progressionin plantain a non-invasive manner. Here, we describe a phenotyping setup and Python image analysis pipeline capturing the Xcc infection in 16Arabidopsis thalianaplants in parallel over time. The setup used both an RGB to capture disease symptoms and an ultra-sensitive CCD camera to monitor bacterial progression inside the leaves using bioluminescence. We demonstrate that the image analysis pipeline reliably quantifies bacterial growthin plantafor two bacterial species, that is vascular Xcc and the mesophyll pathogenPseudomonas syringaepv. tomato. The resolution of the camera allowed early detection of Xcc in the hydathodes, yielding valuable information on this early stage of the Xcc infection process. The data obtained through the automated image analysis pipeline was robust and validated findings from other bioluminescence imaging methods, while requiring fewer samples. We can thus quantify the resistance level of a large number ofArabidopsis thalianaaccessions and mutant lines to different bacterial strains in a non-invasive manner for phenotypic screenings.
Positive correlations in susceptibility to a diverse panel of viruses across host species
Authors: Imrie Ryan M. , Wallace Megan A. , Longdon Ben
Published: October 2024

Our ability to predict the emergence of novel viruses relies on there being generalisable patterns in the susceptibilities of hosts to novel infections. Studies investigating variation in susceptibility among host species have consistently shown that closely related hosts share similar susceptibilities to a given virus. However, the extent to which such phylogenetic patterns of susceptibility are correlated amongst diverse sets of viruses is unclear. Here, we investigate phylogenetic correlations in susceptibility amongDrosophilidaehosts to a panel of eleven different invertebrate viruses, comprising seven unique virus species, six unique families, and both RNA and DNA viruses. The susceptibility of hosts to each pair of viruses tested was either positively correlated across host species or did not show evidence of correlation. No negative correlations, indicative of evolutionary trade-offs in host susceptibility to different viruses, were detected between any virus pairs. The strength of correlations were generally higher in viruses of the same species and family, consistent with virus phylogenetic patterns in host infectivity. Our results suggest that generalised host susceptibility can result in positive correlations, even between highly diverged viruses, while specialised interactions with individual viruses cause a stepwise decrease in correlation strength between viruses from the within-species, to the within-family, to the across-family level.
Growth Rate Assessed by Vascular Deformation Mapping predicts Type B Aortic Dissection in Marfan Syndrome
Authors: Campello Jorge Carlos Alberto , Marway Prabhvir Singh , Tjahjadi Nicasius S , Knauer Heather A , Patel Himanshu J , Hofmann Bowman Marion , Eagle Kim , Burris Nicholas S.
Published: October 2024

Background

Patients with Marfan syndrome (MFS) are at a high risk of type B dissection (TBAD). Aortic growth and elongation have been suggested as risk factors for TBAD. Vascular deformation mapping (VDM) is an image analysis technique for mapping 3D aortic growth on rouine computed tomography angiography (CTA) scans. We aimed to use VDM to examine the value of aortic growth rate in the descending thoracic aorta (DescAo), among other imaging biomarkers, to identify the factors associated with risk of TBAD in MFS.

Methods and Results

CTA scans spanning 2004-2023 from adult MFS patients with native DescAo were analyzed by VDM. Other measurements included multi-level thoracoabdominal aortic diameters and the length of the DescAo by centerline analysis.

Among the 105 MFS patients analyzed, 63.8% were male, with median age of 40 years (range 18-73) and a median surveillance interval of 5.3 years (range 2.0-18.3). During surveillance, 12 (11.4%) patients developed TBAD. Patients with TBAD had higher radial growth rate (0.63 vs. 0.23 mm/year;p< 0.001) and elongation rate (2.4 vs. 0.5 mm/year;p< 0.001), on univariate and multivariable analysis, but pre-dissection descending aortic diameter was not significantly different. Predictors of growth rate included younger age, higher baseline maximal diameter of the DescAo, smoking history and warfarin use.

Conclusions

Radial growth and elongation rates of the DescAo were independent predictors of TBAD occurrence in MFS. TBAD often occurred in at non-aneurysmal diameters (<4.0 cm). These findings emphasize the role of growth over absolute diameter in risk stratification for TBAD in MFS.
Identification of Hub Genes and CDK1-Targeting Therapeutics in Hepatocellular Carcinoma: Bioinformatics and Simulation Study
Authors: Romero Ricardo , Toledo Cinthia C.
Published: October 2024

Background

Hepatocellular carcinoma (HCC) remains a significant global health challenge, often associated with chronic hepatitis B (HBV) and hepatitis C (HCV) infections. Novel therapeutic approaches are urgently needed to improve patient outcomes.

Objective

To identify and validate potential therapeutic targets and novel drug candidates for HBV, HCV, and associated HCC using integrative bioinformatics and molecular dynamics simulations.

Methods

Gene expression datasets from HCC studies were analyzed to identify dysregulated genes. Protein-protein interaction networks were constructed to determine hub genes. Virtual screening of kinase compound libraries against CDK1 was performed, followed by molecular docking and dynamics simulations. Drug-likeness and metabolic properties of hit compounds were evaluated.

Results

Seven hub genes were identified, including five upregulated (CDK1, AURKB, CCNA2, BUB1B, RRM2) and two downregulated (AGXT2, ESR1) genes. Virtual screening yielded three promising hit compounds (G213-0272, E130-0174, Z666960592) targeting CDK1. E130-0174 demonstrated the most favorable profile, with stable CDK1 binding and no inhibition of major cytochrome P450 enzymes. Two repurposed drugs, alvocidib and riviciclib, also showed potential as CDK1 inhibitors.

Conclusions

This study identified novel CDK1 inhibitors with promising profiles for HCC treatment. The integrative approach combining bioinformatics and molecular dynamics simulations provides a robust framework for identifying potential therapeutic targets and drug candidates in HCC and related liver diseases. Further experimental validation is warranted to confirm these findings and advance the development of new HCC treatments.
Estrogen Receptor 1 Signaling in Hepatic Stellate Cells Designates Resistance to Liver Fibrosis
Authors: Li Tianhao , Wang Gang , Zhao Han , Liu Fuhai , Chen Dingbao , Zhou Xin , Deng Zhangyuzi , Cao Ying , Fu Wei , Zhang Haoyue , Yang Jing
Published: October 2024

The prevalence and severity of liver fibrosis appear higher in men than in premenopausal women, while postmenopausal women exhibit the worsened disease. However, the pathophysiological mechanism underlying such clinical observations remains incompletely understood. Here, we show that sex hormone depletion in adult female mice exaggerates the model of liver fibrosis, while estradiol replacement in castrated male mice is sufficient to mitigate the disease severity. Transcriptomic analyses and immunohistochemistry then demonstrate that both human and mouse hepatic stellate cells (HSCs), the primary cell type responsible for extracellular fibrous depositions, predominantly express the estrogen receptor 1 (ESR1). Of importance, genetic deletion of ESR1 in mouse HSCs markedly promotes liver fibrosis. Moreover, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and in vitro manipulations reveal that ESR1 can directly target the expression of fibrosis-related genes in HSCs. Together, this study has elucidated a critical aspect of ESR1 signaling in the sexual dimorphism of liver fibrosis.
Uncovering Latent Biological Function Associations through Gene Set Embeddings
Authors: Huang Yuhang , Zhong Fan
Published: October 2024

The complexity of biological systems has increasingly been unraveled through computational methods, with biological network analysis now focusing on the construction and exploration of well-defined interaction networks. Traditional graph-theoretical approaches have been instrumental in mapping key biological processes using high-confidence interaction data. However, these methods often struggle with incomplete or/and heterogeneous datasets. In this study, we extend beyond conventional bipartite models by integrating attribute-driven knowledge from the Molecular Signatures Database (MSigDB) using the node2vec algorithm. Our approach explores unsupervised biological relationships and uncovers potential associations between genes and biological terms through network connectivity analysis. By embedding both human and mouse data into a shared vector space, we validate our findings cross-species, further strengthening the robustness of our method. This integrative framework reveals both expected and novel biological insights, offering a comprehensive perspective that complements traditional biological network analysis and paves the way for deeper understanding of complex biological processes and diseases.
Noncovarying storage effect: balancing and positive directional selection on mutant alleles that amplify random fitness and demographic fluctuations
Authors: Kim Yuseob
Published: October 2024

Temporally variable environments in natural populations generate fluctuations in not only the population size but also the fitness effects of mutant alleles. The theory of storage effect, a species/allelic diversity-promoting mechanism discovered in ecology, predicts that rare mutants with fluctuating fitness can be positively selected and then maintained in balanced polymorphism if the population is subdivided into two parts that are respectively exposed to and protected from fluctuating environment. Recent study found that, under pre-exisiting oscillation in population size, the mutant is positively selected to fixation if its fitness change correlates with the rate of population growth, which further amplifies population size oscillation. To further understand these eco-evolutionary dynamics and elucidate their generality in natural populations, this study built more realistic models that assume randomly, not cyclically, fluctuating selection and common demographic features, including heterogeneous ecological patches or an age-structured population. Mathematical analysis revealed that this novel evolutionary force is generated when the size of the subpopulation subject to weak selection does not covary with that of the other subpopulation. Simulations showed that this ‘noncovarying storage effect’ is robust to various perturbations in the model. Multi-locus simulations revealed that oscillatory polymorphism at many loci can be simultaneously maintained and that positive feedback between demography and selection can accelerate the sequential fixations of fluctuation-amplifying mutations and thus lead to a drastic amplification of population size fluctuation. These results suggest that the noncovarying storage effect is a potentially prevalent evolutionary force in nature for maintaining genetic variation and causing large demographic fluctuations.

ARTICLE SUMMARY

Natural populations experience rapid environmental changes that cause fluctuations in the fitness of genetic variants and population size. This study investigates how evolutionary changes due to fitness differences interact with concurrent demographic changes. The theory of the storage effect, which is a mechanism for promoting genetic diversity, was extended to add random population size fluctuation with heterogeneous environmental patches or in a population divided into different age classes. A novel evolutionary force that either increases genetic variation or drives evolution toward further amplification of population size fluctuation, an unconventional contributor to large demographic fluctuations in nature, was identified and analyzed.
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

The 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

Obesity 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 abstract

Highlights

Obesity 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

Background and Aims

Sporopollenin (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.

Methods

We 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 Results

We 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.

Conclusions

The 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

It 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

Unprecedented 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

Pigs 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

Gene 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

Herein, 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.
Intrinsic functional connectivity of right dorsolateral prefrontal cortex and hippocampus subregions relates to emotional and sensory-perceptual properties of intrusive trauma memories
Authors: Devignes Quentin , Clancy Kevin J , Ren Boyu , Pollmann Yara , Baker Justin T , Rosso Isabelle M
Published: October 2024

Background: Trauma-related intrusive memories (TR-IMs), unwanted and vivid, are core symptoms of posttraumatic stress disorder (PTSD). Prior research links voluntary TR-IM suppression to inhibitory control of the right dorsolateral prefrontal cortex (dlPFC) over the hippocampus (HPC). However, the potential relevance of tonic resting-state inhibition has not been examined, nor has the functional differentiation of the anterior and posterior hippocampus (aHPC/HPC). This study examined relationships of TR-IM frequency and properties with resting-state negative coupling between the right dlPFC and right aHPC/pHPC in trauma-exposed individuals with PTSD symptoms. Methods: Participants (N=109; 88 female) completed two weeks of ecological momentary assessments capturing TR-IM frequency and properties (intrusiveness, emotional intensity, vividness, visual properties, and reliving). Using 3T resting-state magnetic resonance imaging, participant-specific 4-mm spheres were placed at the right dlPFC voxel most anticorrelated with the right aHPC and pHPC. Quasi-Poisson and linear mixed-effects models assessed relationships of TR-IM frequency and properties with right dlPFC-right aHPC and pHPC anticorrelation. Results: TR-IM emotional intensity was positively associated with right dlPFC-aHPC connectivity, while vividness and visual properties were linked to right dlPFC-pHPC connectivity. No significant associations were found between TR-IM frequency, intrusiveness, or reliving, and anticorrelation with either HPC subregion. Conclusions: This study provides novel insights into the neural correlates of TR-IMs, highlighting the relevance of intrinsic negative coupling between the right dlPFC and aHPC/pHPC to their emotional impact and perceptual properties. Further research on inhibitory mechanisms in this circuit could improve understanding of component processes of intrusive reexperiencing, a severe and treatment-refractory PTSD symptom.
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

Throughout 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

Objective

This 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.

Methods

We 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.

Results

In 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).

Conclusion

As 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

The 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

Background

History 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.

Methods

MR 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.

Results

Genetically 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).

Conclusion

This MR study supports a causative link betweenC. trachomatisinfection and overall and high-grade serous EOC.
Neuronal mechanisms of adaptive value coding in the amygdala
Authors: Hinz Julian , Mahn Mathias , Müller Sigrid , Szőnyi András , Eichlisberger Tobias , Lüthi Andreas
Published: October 2024

To address their needs, animals must optimize behavior by integrating external cues with internal state signals, such as hunger or thirst, environmental conditions, and past experiences. Accordingly, the perceived value of a reward varies depending on an animal’s current needs. Updating the specific value of rewards predicted by external cues depends on the basolateral amygdala (BLA). However, neurophysiological investigations have centered around the assumption of stimulus-invariant value representations and have not been able to account for behavioral findings that support the BLA’s ability to represent stimulus-specific value of distinct appetitive or aversive outcomes. To address how the BLA encodes and updates stimulus-specific value representations, we exposed head-fixed mice to distinct sets of gustatory rewards while tracking perceived value using lick microstructural analysis. Two-photon calcium imaging of BLA principal neurons revealed that the magnitude of the BLA population response scaled with perceived reward value and that the values of different rewards were encoded by distinct neuronal subpopulations. Moreover, reward representations rapidly re-scaled when mice were exposed to a reward that was larger than all previous rewards. Finally, value representations depended on an animal’s internal state as thirst selectively increased the responses to water rewards whereas aversive experiences strongly attenuated responses to sucrose. Our findings demonstrate that value representations in the BLA are stimulus-specific and highly adaptive to account for changes in relative reward value and to reflect an animal’s current affective and homeostatic state. This mechanism enables sensory-specific value updates necessary for state-adapted decision making and learning.