bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel comparison reveals conservation and re-wiring of abiotic stress response networks across three plant species
Authors: Lee Jia Min , Goh Jong Ching , Mutwil-Anderwald Daniela , Mutwil Marek 
Published: April 2024

AbstractAbiotic stresses trigger significant alterations in plant morphology, yield, and nutrient composition. To counter these stresses, plants have developed strategies involving gene expression adjustments, impacting their growth and development to ensure survival and reproduction. Although transcriptomic studies have extensively examined stress responses, our understanding of their conservation remains limited. We conducted a comprehensive study on the effects of 24 different environmental and nutrient conditions on the growth yield of three hydroponically grown leafy crops (cai xin, lettuce, and spinach). This research identified optimal conditions for maximizing yield and vitamin content and pinpointed conditions that induce abiotic stress. Our findings highlight the substantial impact of stress on various plant functions, with photosynthesis playing a pivotal role in vitamin content regulation. A detailed comparative analysis of gene expression across these crops revealed conserved gene sets potentially crucial for abiotic stress response. Furthermore, we introduced a novel method that merges regression and genomics to construct reliable gene regulatory networks for stress response. Despite significant conservation of these networks among the studied crops, their key transcription factors showed limited similarity to those inArabidopsis thaliana, suggesting notable functional divergence. To give easy access to the data and comparative transcriptomic tools, we established StressPlantTools, an public online database (https://stress.sbs.ntu.edu.sg/), facilitating further research into stress-responsive genes.
Wax “tails” enable planthopper nymphs to self-right midair and land on their feet
Authors: McDonald Christina L. , Alcalde Gerwin T. , Jones Thomas C. , Laude Ruby Ana P. , Yap Sheryl A. , Bhamla M. Saad 
Published: April 2024

AbstractThe striking appearance of wax ‘tails’ — posterior wax projections on planthopper nymphs — has captivated entomologists and naturalists alike. Despite their intriguing presence, the functional roles of these structures remain largely unexplored. This study leverages high-speed imaging to uncover the biomechanical implications of these wax formations in the aerial dynamics of planthopper nymphs (Ricania sp.). We quantitatively demonstrate that removing wax tails significantly increases body rotations during jumps. Specifically, nymphs without wax projections undergo continuous rotations, averaging 4.3±1.9 per jump, in contrast to wax-intact nymphs, who narrowly complete a full rotation, averaging only 0.7±0.2 per jump. This suggests that wax structures effectively counteract rotation through aerodynamic drag forces. These stark differences in body rotation correlate with landing success: nymphs with wax intact achieve a near perfect landing rate of 98.5%, while those without wax manage only a 35.5% success rate. Jump trajectory analysis reveals transitions from parabolic to Tartaglia shapes at higher take-off velocities for wax-intact nymphs, illustrating how wax structures assist nymphs in achieving stable, controlled descents. Our findings confirm the aerodynamic self-righting functionality of wax tails in stabilizing planthopper landings, advancing our understanding of the complex interplay between wax morphology and aerial maneuverability, with broader implications for the evolution of flight in wingless insects and bioinspired robotics.
Virophage replication mode determines ecological and evolutionary changes in a host-virus-virophage system
Authors: del Arco Ana , Becks Lutz 
Published: April 2024

AbstractGiant viruses can control their eukaryotic host populations, shaping the ecology and evolution of aquatic microbial communities. Understanding the impact of the viruses’ own parasites, the virophages, on their control of microbial communities remains a challenge. Most virophages have two modes of host infection and replication. They can exist as free particles that co-infect a host cell with the virus and replicate but inhibit viral replication. Virophages can also integrate into the host genome and remain dormant until the host is infected with a virus, leading to virophage reactivation and replication that does not immediately inhibit viral replication. Both replication modes are present within host-virus-virophage communities, and their relative contributions are expected to be context dependent and dynamic over time. The consequences of this dynamic regime for ecological and evolutionary dynamics remain unexplored. Here, we test whether and how the relative contribution of virophage replication modes influences the ecological dynamics of an experimental host-virus-virophage system and the evolutionary responses of the virophage. To do this, we indirectly manipulated the level of virophage (Mavirus) integration into the host (Cafeteria burkhardae) in the presence of the giant Cafeteria roenbergensis virus (CroV) (later identified asCafeteria burkhardae, Schoenle et al. 2020). Our results show that higher virophage integration is positively correlated with host survival, but negatively correlated with virophage reactivation. In addition, communities with higher virophage integration were characterised by lower population densities and reduced fluctuations in both host and viral populations, whereas virophage fluctuations were increased. This study reveals the complex interplay between virophages, viruses and hosts, in which the virophage dual replication mode is a dynamic and reactive mechanism contributing to persistence of the microbial community.
Sex-specific recombination landscape in a species with holocentric chromosomes
Authors: Chmielewski Sebastian , Konczal Mateusz , Parrett Jonathan M. , Rombauts Stephane , Dudek Katarzyna , Radwan Jacek , Babik Wiesław 
Published: April 2024

AbstractThe rate and chromosomal positioning of meiotic recombination significantly affects the distribution of the genetic diversity in eukaryotic genomes. Many studies have revealed sex-specific recombination patterns, with male recombination typically biased toward chromosome ends, while female recombination is more evenly distributed along chromosomes, or concentrated near the chromosome center. It has been proposed that such pattern in females may counteract meiotic drive caused by selfish genetic elements near centromeres and should not occur in species devoid of clearly defined centromeres, but evidence for the latter is scarce. Here, we constructed a sex-specific genetic map of a species with holocentric chromosomes, the bulb mite (Rhizoglyphus robini), a sexual selection model with alternative male reproductive phenotypes. We found a similar recombination landscape in both males and females, with a consistent pattern of increased rates towards both chromosome ends, and higher recombination rate in females than in males. A region on chromosome 7, carrying a high density of markers associated with the expression of alternative male reproductive phenotypes, was among several regions with particularly low male recombination rate. We detected a positive correlation between the recombination rate and the repeat density (highest at chromosome ends), and negative correlation with the gene density (peaking at chromosome centers). Our results are consistent with the meiotic drive hypothesis and suggest that recombination evolution is closely linked to the chromosome features.
Protein codes promote selective subcellular compartmentalization
Authors: Kilgore Henry R. , Chinn Itamar , Mikhael Peter G. , Mitnikov Ilan , Van Dongen Catherine , Zylberberg Guy , Afeyan Lena , Banani Salman , Wilson-Hawken Susana , Lee Tong Ihn , Barzilay Regina , Young Richard A. 
Published: April 2024

AbstractCells have evolved mechanisms to distribute ∼10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must efficiently assemble. Here, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. A protein language model, ProtGPS, was developed that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in targeted subcellular compartments. ProtGPS also identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code, but also a previously unrecognized code governing their distribution in specific cellular compartments.
Neural Dynamics During the Generation and Evaluation of Creative and Non-Creative Ideas
Authors: Kenett Yoed N. , Chrysikou Evangelia G. , Bassett Dani S. , Thompson-Schill Sharon L. 
Published: April 2024

AbstractWhat are the neural dynamics that drive creative thinking? Recent studies have provided much insight into the neural mechanisms of creative thought. Specifically, the interaction between the executive control, default mode, and salience brain networks has been shown to be an important marker of individual differences in creative ability. However, how these different brain systems might be recruited dynamically during the two key components of the creative process— generation and evaluation of ideas—remains far from understood. In the current study we applied state-of-the-art network neuroscience methodologies to examine the neural dynamics related to the generation and evaluation of creative and non-creative ideas using a novel within-subjects design. Participants completed two functional magnetic resonance imaging sessions, taking place a week apart. In the first imaging session, participants generated either creative (alternative uses) or non-creative (common characteristics) responses to common objects. In the second imaging session, participants evaluated their own creative and non-creative responses to the same objects. Network neuroscience methods were applied to examine and directly compare reconfiguration, integration, and recruitment of brain networks during these four conditions. We found that generating creative ideas led to significantly higher network reconfiguration than generating non-creative ideas, whereas evaluating creative and non-creative ideas led to similar levels of network integration. Furthermore, we found that these differences were attributable to different dynamic patterns of neural activity across the executive control, default mode, and salience networks. This study is the first to show within-subject differences in neural dynamics related to generating and evaluating creative and non-creative ideas.
An optogenetic assay for the dauer decision in Caenorhabditis elegans
Authors: Parker Ariel , Mullins James , Corver Abel , Miller Anastasia , Mosley Iman , Gordus Andrew 
Published: April 2024

AbstractThe dauer decision inCaenorhabditis elegansis a critical developmental decision that ensures survival under harsh environmental conditions. Factors such as temperature, food availability, and pheromone strongly influence the decision to enter and exit dauer. Traditional assays that assess the dauer decision are often confounded by the influence of pheromones from the population, which are often dynamic and highly variable. To mitigate this issue, we developed a simple, single-housing assay for dauer quantification that is compatible with optogenetics. We show that insulin-like peptides (ILPs) from ASJ and other neurons strongly influence the decision to exit dauer, and that ASJ activity can be manipulated with optogenetics to influence the dauer decision in a temporally precise manner.
Paired transcriptomic analyses of atheromatous and control vessels reveal novel autophagy and immunoregulatory genes in peripheral artery disease
Authors: Machiraju Praveen , Srinivas Rajesh , Kannan Ramraj , George Robbie , Heymans Stephane , Mukhopadhyay Rupak , Ghosh Arkasubhra 
Published: April 2024

AbstractBackgroundPeripheral artery disease (PAD), a significant health burden worldwide, affects lower extremities due to atherosclerotic changes in the peripheral vessels. Although mechanisms of PAD have been studied, the molecular milieu of the plaques localized within peripheral arteries in patients are not well understood. Thus, to identify PAD lesion specific gene expression profiles precluding genetic, environmental and dietary biases, we studied the transcriptomic profile of plaque tissues normalized to non-plaque tissues from the same donors.MethodsTranscriptomic analysis of 9 paired samples of PAD patients from south Indian population was performed with institutional ethics approval and written consent. Plaque tissues were histologically confirmed. Expression of a select target gene set was done by qPCR from the same tissues. Bioinformatic and network analyses were performed using various statistical tools.ResultsA total of 296 upregulated, 274 downregulated genes and 186 non-coding RNAs were identified. STAG1, SPCC3, FOXQ1 and E2F3 were key downregulated genes and CD93 was top upregulated gene. Autophagosome assembly, cellular response to UV, cytoskeletal organization, TCR signaling and phosphatase activity were key dysregulated pathways identified in the study. Telomerase regulation and autophagy were identified as novel interacting pathways using network analysis. Plaque tissue was predominantly composed of immune cells and dedifferentiated cell populations indicated by cell specific marker imputed gene expression analysis.ConclusionThe current study identifies novel genes, non-coding RNAs, associated regulatory pathways and cell composition of the plaque tissue in PAD patients. The autophagy and immunoregulatory genes may drive novel mechanisms resulting in atheroma. These novel interacting networks and genes have the potential for PAD specific therapeutic applications.
Intestinal commensal bacteria promoteBactrocera dorsalislarval development through vitamin B6 synthesis pathway
Authors: Gu Jian , Yao Zhichao , Lemaitre Bruno , Cai Zhaohui , Zhang Hongyu , Li Xiaoxue 
Published: April 2024

AbstractBackgroundThe gut microbiota can facilitate host growth under nutrient-constrained conditions. However, whether this effect is limited to certain bacterial species remains largely unclear, and the relevant mechanisms remain to be thoroughly investigated.ResultsHere, we found that the microbiota was required forBactrocera dorsalislarval growth under poor diet conditions. Mono-association experiments revealed thatEnterobacteriaceaeand someLactobacillipromoted larval growth. Of 27 tested bacterial strains, 15 strains significantly promoted larval development, and theEnterobacteriaceae cloacaeN29 isolate exhibited the most obvious promoting effect. Bacterial genome-wide association study (GWAS) revealed that the vitamin B6 synthesis pathway was critical forE. cloacaegrowth promotion. The deletion ofpdxAresponsible for the vitamin B6 biosynthesis deprived the mutant strains of larval growth promotion function, indicating thatpdxAgene was crucial for promoting larval growth in the N29 strain. Importantly, supplementation of vitamin B6 to poor diet successfully rescued the axenic larval growth phenotype ofB. dorsalis.ConclusionOur results suggest that gut microbes promote insect larval growth by providing vitamin B6 under nutrient scarcity inB. dorsalis.
Determinants of Healthcare Insurance Coverage among Women of Reproductive Age in Tanzania: A Multilevel Mixed Effect Analysis
Authors: Kessy Sanun Ally , Tibenderana Jovin R. , Gimonge Jomo , Moshi Fabiola V 
Published: April 2024

AbstractBackgroundHealth insurance has been one of the fundamental approaches of financing healthcare for sustainable Development goals (SDGs). There is a paucity of evidence on the determinants of healthcare insurance coverage among women of reproductive age in Tanzania, therefore this study aimed at assessing factors associated with access to health care insurance among women of reproductive age in Tanzania using national Demographic and health survey dataset.MethodologyThis study was an analytical cross-sectional study that utilized nationally representative secondary data sourced from the Tanzania Demographic and Health Surveys (TDHS) of 2022.A weighted sample of 15,254 women of reproductive age (15–49) was included in the study. A multilevel regression analysis was used to examine factors associated with health care insurance coverage. These results were presented using adjusted odds ratio (AOR) with a 95% confidence interval.ResultsIn Tanzania the proportion of health insurance coverage among women of reproductive age was 5.8% whereby majority of women subscribing to employer’s insurance (3.9%). Older women (35–49) were more likely to be covered with health insurance compared those aged 15-24 (AOR =2.75, 95% CI: 2.19, 3.45). Similarly, married women had higher likelihood of health insurance coverage compared to unmarried (AOR=1.60, 95% CI: 1.33, 1.92). Furthermore, educated women were more likely to be covered with health insurance than uneducated women (AOR=6.96, 95% CI: 4.74, 10.22). Similarly, women who were exposed to mass media were more likely to be covered with health care insurance compared to unexposed (AOR=1.43, 95% CI: 1.14, 1.78).ConclusionLess than ten percent of Tanzanian women of reproductive age (WRA) are registered in health insurance, which is an unacceptably low coverage. This highlights the urgent need to eliminate barriers preventing this population’s access to healthcare in order to achieve Standard Development Goals (SDGs) by 2030. The interplay of socioeconomic factors and access to information underscores the need for multifaceted approaches to enhance healthcare coverage among women of reproductive age in Tanzania.
Early prediction ofMycobacterium tuberculosistransmission clusters using supervised learning models
Authors: Gharamaleki Omid Gheysar , Colijn Caroline , Sekirov Inna , Johnston James C , Sobkowiak Benjamin 
Published: April 2024

AbstractIdentifying individuals with tuberculosis with a high risk of onward transmission can guide disease prevention and public health strategies. Here, we train classification models to predict the first sampled isolates inMycobacterium tuberculosistransmission clusters from demographic and disease data. We find that supervised learning models, in particular balanced random forests, can be used to develop predictive models that discriminate between individuals with TB that are more likely to form transmission clusters and individuals that are likely not to transmit further, with good model performance and AUCs of ≥ 0.75. We also identified the most important patient and disease characteristics in the best performing classification model, including patient demographics, site of infection, TB lineage, and age at diagnosis. This framework can be used to develop predictive tools for the early assessment of a patient’s transmission risk to prioritise individuals for enhanced follow-up with the aim of reducing further transmission.
Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping
Authors: Kyratzi Panagiota , Matika Oswald , Brassington Amey H , Clare Connie E , Xu Juan , Barrett David A , Emes Richard D , Archibald Alan L , Paldi Andras , Sinclair Kevin D , Wattis Jonathan , Rauch Cyril 
Published: April 2024

ABSTRACTIdentifying associations between phenotype and genotype is the fundamental basis of genetic analyses. Inspired by frequentist probability and the work of R.A. Fisher, genome-wide association studies (GWAS) extract information using averages and variances from genotype-phenotype datasets. Averages and variances are legitimated upon creating distribution density functions obtained through the grouping of data into categories. However, as data from within a given category cannot be differentiated, the investigative power of such methodologies is limited. Genomic Informational Field Theory (GIFT) is a method specifically designed to circumvent this issue. The way GIFT proceeds is opposite to that of GWAS. Whilst GWAS determines the extent to which genes are involved in phenotype formation (bottom-up approach), GIFT determines the degree to which the phenotype can select microstates (genes) for its subsistence (top-down approach). Doing so requires dealing with new genetic concepts, a.k.a. genetic paths, upon which significance levels for genotype-phenotype associations can be determined. By using different datasets obtained inovis ariesrelated to bone growth (Dataset-1) and to a series of linked metabolic and epigenetic pathways (Dataset-2), we demonstrate that removing the informational barrier linked to categories enhances the investigative and discriminative powers of GIFT, namely that GIFT extracts more information than GWAS. We conclude by suggesting that GIFT is an adequate tool to study how phenotypic plasticity and genetic assimilation are linked.NEW & NOTEWORTHYThe genetic basis of complex traits remains challenging to investigate using classic GWASs. Given the success of gene editing technologies this point needs to be addressed urgently since there can only be useful editing technologies if precise genotype-phenotype mapping information is available initially. GIFT is a new mapping method designed to increase the investigative power of biological/medical datasets suggesting, in turn, the need to rethink the conceptual bases of quantitative genetics.