bluuebunny/crossref_metadata_2025_split huggingface dataset:
Notch1 and Notch2 Signaling Exclusively but Cooperatively Maintain Fetal Myogenic Progenitors
Authors: Jo Young-Woo , Park Inkuk , Yoo Kyusang , Woo Hyun-Young , Kim Ye Lynne , Kim Yea-Eun , Kim Ji-Hoon , Kong Young-Yun 
Published: August 2022

Abstract
Myogenic progenitors (MPs) generate myocytes that fuse to form myofibers during skeletal muscle development while maintaining the progenitor pool, which is crucial for generating sufficient muscle. Notch signaling has been known to reserve a population of embryonic MPs during primary myogenesis by promoting cell cycle exit and suppressing premature differentiation. However, the roles of individual Notch receptors (Notch1-4) during embryonic/fetal myogenesis are still elusive. In this study, we found that Notch1 and Notch2, which exhibit the highest structural similarity among Notch receptors, maintain the MP population by distinct mechanisms: Notch1 induces cell cycle exit and Notch2 suppresses premature differentiation. Moreover, genetic and cell culture studies showed that Notch1 and Notch2 signaling in MPs are distinctively activated by interacting with Notch ligand-expressing myofibers and MP-lineage cells, respectively. These results suggest that through different activation modes, Notch1 and Notch2 distinctively and cooperatively maintain MP population during fetal myogenesis for proper muscle development.
Transcriptome Response of Cannabis (Cannabis sativa L.) to the Pathogenic fungus Golovinomyces ambrosiae
Authors: Adhikary Dinesh , El-Mezawy Aliaa , Khatri-Chhetri Upama , Wu Limin , Smith Stephen W. , Zhang Jian , Slaski Jan J. , Kav Nat N.V. , Deyholos Michael K. 
Published: August 2022

AbstractPowdery mildew (PM), caused by the obligate biotrophic fungus Golovinomyces ambrosiae, is an economically important fungal disease of hemp - and marijuana–type cannabis. While the PM disease can be managed effectively by cultivating resistant hosts, there is no known PM-resistant genetic variant. This is the first report of transcript level responses of the hemp cultivar ‘X59’ to G. ambrosiae. Transcript level changes at 5-, 8-, and 11-days post-inoculation (DPI) of C. sativa were evaluated against uninoculated control. Our analysis revealed that 1,898 genes were significantly (q-value < 0.05) differentially expressed (DE) following the pathogen challenge. Among these, 910 and 988 genes were upregulated and downregulated, respectively as the infection progressed to 11 DPI. Genes related to salicylic acid (SA), (LOC115715124 and LOC115711424) and WRKY transcription factor (LOC115707546, LOC115715968, and LOC115707511) were highly upregulated. There were 45 DEGs that were homologous to PM-related genes, including chitin elicitor receptor kinase 1 (CERK 1), enhanced disease resistance 2, (EDR2), and powdery mildew resistance (PMR) genes. Moreover, the genes related to glycosyl hydrolases, particularly LOC115699396, LOC115708023, LOC115710105, and LOC115710100, were highly upregulated and potentially important in mediating pathogen responses. Collectively, this study has contributed to an enhanced understanding of the molecular mechanisms that are involved in cannabis and PM disease interaction and has identified several gene candidates that can be further investigated for their role in defence mechanisms.
A Web-scraped Skin Image Database of Monkeypox, Chickenpox, Smallpox, Cowpox, and Measles
Authors: Islam Towhidul , Hussain Mohammad Arafat , Chowdhury Forhad Uddin Hasan , Islam B. M. Riazul 
Published: August 2022

AbstractMonkeypox has emerged as a fast-spreading disease around the world and an outbreak has been reported in 75 countries so far. Although the clinical attributes of Monkeypox are similar to those of Smallpox, skin lesions and rashes caused by Monkeypox often resemble those of other types of pox, for example, chickenpox and cowpox. This scenario makes an early diagnosis of Monkeypox challenging for the healthcare professional just by observing the visual appearance of lesions and rashes. The rarity of Monkeypox before the current outbreak further created a knowledge gap among healthcare professionals around the world. To tackle this challenging situation, scientists are taking motivation from the success of supervised machine learning in COVID-19 detection. However, the lack of Monkeypox skin image data is making the bottleneck of using machine learning in Monkeypox detection from patient skin images. Therefore, in this project, we introduce the Monkeypox Skin Image Dataset 2022, the largest of its kind so far. We used web-scraping to collect Monkeypox, Chickenpox, Smallpox, Cowpox, and Measles infected skin as well as healthy skin images to build a comprehensive image database and make it publicly available. We believe that our database will facilitate the development of baseline machine learning algorithms for early detection of Monkeypox in clinical settings. Our dataset is available at the following Kaggle link: https://www.kaggle.com/datasets/arafathussain/monkeypox-skin-image-dataset-2022.
Prosperity of the commons: Generalist mycorrhizal species dominate a mixed forest and may promote forest diversity by mediating resource sharing among trees
Authors: Rog Ido , Lewin-Epstein Ohad , Livne-Luzon Stav , Hadany Lilach , Klein Tamir 
Published: August 2022

AbstractMechanisms of host–microbe interactions and their direct impact on both parties have been extensively researched, however, much less is known on the effect of these interactions on the ecology of the host-community. Here we investigate tree-fungi mycorrhizal interactions, focusing on mycorrhizal-mediated resource sharing among trees, while examining the dynamics between specialist and generalist fungi and their implications on the forest ecology. Using genetic meta-barcoding, we identified the fungal community colonizing different trees in a mixed forest, and generated an extensive mapping connecting fungal sequences to their tree hosts. The mycorrhizal fungal community diverged between ectomycorrhizal and arbuscular host trees, but, unexpectedly, multiple ectomycorrhizal species colonized roots of non-ectomycorrhizal host trees. We complemented these findings by a novel computational framework, modeling competition between generalist and specialist mycorrhizal fungi, accounting for fungal-mediated resource sharing among neighboring trees. The analysis of the model revealed that generalist mycorrhizal networks may affect the entire tree community, and contribute to the maintenance of forest diversity in the long run. Furthermore, higher initial spatial mixing of trees can promote the evolution of generalist mycorrhizal species. These novel belowground interactions among trees and fungi may significantly impact forest biodiversity.
Geographic variability of hybridization between Red-breasted and Red-naped Sapsuckers
Authors: Natola Libby , Billerman Shawn M. , Carling Matthew D. , Seneviratne Sampath S. , Irwin Darren 
Published: August 2022

AbstractHybrid zones reveal the strength of reproductive isolation between populations undergoing speciation and are thus a key tool used in evolutionary biology research. Multiple replicate transects across the same hybrid zone offer further insight into the dynamics of hybridization in different environments, clarifying the role of extrinsic forces on the speciation process. Red-breasted and Red-naped Sapsuckers (Sphyrapicus ruber and S. nuchalis) have a long zone of contact over approximately 1,600 km from central British Columbia, Canada to central California, USA. We compared Genotyping-by-Sequencing data from three independent sapsucker hybrid zone transects to compare hybridization dynamics between the same species under variable geoclimatic conditions. We then generated geographic clines of the genomic data to compare hybrid zone widths and used Random Forest models and linear regression to assess the relationship between climate and sapsucker ancestry along each transect. Our results show variation in symmetry and directionality of back crossing, patterns often indicative of moving hybrid zones. We note variable cline widths among transects, indicating differences in the selection maintaining hybrid zone dynamics. Furthermore, Random Forest models identified different variables in close association with sapsucker ancestry across each transect. These results indicate a lack of repeatability across replicate transects and a strong influence of the local environment on hybrid zone dynamics.
Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory networks
Authors: Puzović Nataša , Madaan Tanvi , Dutheil Julien Y. 
Published: August 2022

AbstractExpression noise, the variability of the amount of gene product among isogenic cells grown in identical conditions, originates from the inherent stochasticity of diffusion and binding of the molecular players involved in transcription and translation. It has been shown that expression noise is an evolvable trait and that central genes exhibit less noise than peripheral genes in gene networks. A possible explanation for this pattern is increased selective pressure on central genes since they propagate their noise to downstream targets, leading to noise amplification. To test this hypothesis, we developed a new gene regulatory network model with inheritable stochastic gene expression and simulated the evolution of gene-specific expression noise under constraint at the network level. Stabilizing selection was imposed on the expression level of all genes in the network and rounds of mutation, selection, replication and recombination were performed. We observed that local network features affect both the probability to respond to selection, and the strength of the selective pressure acting on individual genes. In particular, the reduction of gene-specific expression noise as a response to stabilizing selection on the mean expression is higher in genes with higher centrality metrics. Furthermore, global topological structures such as network diameter, centralization and average degree affect the average expression variance and average selective pressure acting on constituent genes. Our results demonstrate that selection at the network level leads to differential selective pressure at the gene level, and local and global network characteristics are an essential component of gene-specific expression noise evolution.
Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments
Authors: Chamberlin John T. , Lee Younghee , Marth Gabor T. , Quinlan Aaron R. 
Published: August 2022

AbstractA mechanistic understanding of the biological and technical factors that impact cell and nuclear transcript measurements is essential to designing, analyzing, and interpreting single-cell and single-nucleus RNA sequencing experiments. RNA sampling in nuclei and cells is fundamentally different as nuclei contain the same pre-mRNA population as cells, yet contain a small subset of the largely-cytoplasmic mRNAs. Nonetheless, early studies argued that including pre-mRNA in single-nucleus analysis led to results comparable to cellular samples. However, typical bioinformatic workflows do not distinguish between pre-mRNA and mRNA when analyzing gene expression, and variation in the relative abundance of pre-mRNA and mRNA across cell types has received limited attention. These gaps are especially important given that incorporating pre-mRNA in routine gene expression analysis is now commonplace for both assays, despite known gene length bias in pre-mRNA capture. Here, we reanalyze public datasets from mouse and human to describe the mechanisms and contrasting effects of mRNA and pre-mRNA sampling in single-cell and nucleus RNA-seq. We disentangle the roles of bioinformatic processing, assay choice, and biological variability on measured gene expression and marker gene selection. We show that pre-mRNA levels vary considerably among cell types, which mediates the degree of gene length bias within and between assays and limits the generalizability of a recently-published normalization method intended to correct for this bias. As an alternative solution, we demonstrate the applicability of an existing post hoc gene length-based correction method developed for conventional RNA-seq gene set enrichment analysis. Finally, we show that the inclusion of pre-mRNA in bioinformatic processing can impart a larger effect on gene expression estimates than the choice of cell versus nuclear assay, which is pivotal to the effective reuse of existing data. Broadly, these analyses advance our understanding of the biological and technical factors underlying variation in single-cell and single-nucleus RNA-seq experiments to promote more informed choices in experimental design, data analysis, and data sharing and reuse.
ioSearch: a tool for searching disease-associated interacting omics; application on breast cancer data
Authors: Das Sarmistha , Srivastava Deo Kumar 
Published: August 2022

AbstractBiomarkers identification is difficult for cancer and other polygenic traits because such complicated diseases occur due to an intricate interplay of various genetic materials. Although high-throughput data from recent technolo-gies provide access to a tremendous amount of information still there is a huge gap in harnessing knowledge from the generated multi-omics data. It is evident from the availability of subject-specific multi-omics data from large consortiums that there is a growing need for appropriate tools to analyze such data. Traditional single-omics association tests more often identify strong signals but fail to explore the between-omics relationship and find moderately weak signals due to multiple testing burdens. Multi-omics data integration intuitively provides a clear advantage in understanding the genetic architecture of disease a little better by imparting complementary information. But the construction of such methods is challenging because of the diversity in the nature of multiple omics and the sample size which is much less than the number of omics variables. It is important to consider factors such as data diversity and prior biological knowledge to make meaningful and better predictions. Dimension reduction techniques such as feature selection are used to circumvent the sample size issue in general but treating all the omics variables similarly might be an oversimplification of the complex biological interactions. The lack of appropriate approaches for biomarker identification from complex multi-omics data led us to develop this method. ioSearch is a tool for integrating two omics assays with continuous measurements. Based on a two-step model, ioSearch explores the inter-relationship of the omics in a principal regression framework and selects features using sparse principal component analysis to provide easily interpretable inference in terms of p-values. Also, it uses prior biological information to reduce multiple testing burdens. Extensive simulation results show that our method is statistically powerful with a controlled type I error rate. Application of ioSearch to two publicly available breast cancer datasets identified relevant genes and proteins in important pathways.
Is there a trade-off between host generalism and aggressiveness across pathogen populations? A synthesis of the global potato and tomato blight lesion growth data
Authors: Wan Justin SH 
Published: August 2022

AbstractPhytophthora infestanspopulations and lineages vary widely in host specificity from specialisation to generalism among potato and tomato. However, generalists that displace others and became dominant on both hosts are relatively uncommon. Generalists may have lower fitness compared to specialists on the host of the latter, which could explain their coexistence at many locations. Lesion size is an aggressiveness metric closely related to fitness inP. infestans. A trade-off between generalism and lesion growth rate on the original host can explain the variation among blight populations. I collated the data from cross-inoculation trials on potato and tomato isolates to test for the trade-off. In addition, other metrics related to disease symptoms were included to test whether the degree of specificity is different between populations from potato and tomato, and to explore whether specificity had changed over time. The results indicate a trade-off between generalism and lesion growth rate where higher specificity was associated with significantly faster lesion growth on the original host at the population-level, but not at the lineage-level. Potato and tomato isolates were overall not significantly different in specificity, but tomato isolates tended towards generalism with time. These findings indicate that specialists may avoid displacement on their host by generalists through faster lesion growth, and help explain the common co-occurrence of generalists and specialists. However, a few invasive generalists can rapidly displace competitors and became dominant on both hosts across a broader region. It is likely that important exceptions exist to this trade-off.
A greenhouse-based high-throughput phenotyping platform for identification and genetic dissection of resistance to Aphanomyces root rot in field pea
Authors: Al Bari Md. Abdullah , Fonseka Dimitri , Stenger John , Zitnick-Anderson Kimberly , Atanda Sikiru Adeniyi , Worral Hannah , Piche Lisa , Kim Jeonghwa , Morales Mario , Johnson Josephine , Saludares Rica Amor , Flores Paulo , Pasche Julie , Bandillo Nonoy 
Published: August 2022

AbstractAphanomyces root rot (ARR) is a devastating disease in field pea(Pisum sativumL.) that can cause up to 100% crop failure. Assessment of ARR resistance can be a rigorous, costly, time-demanding activity that is relatively low-throughput and prone to human errors. These limits the ability to effectively and efficiently phenotype the disease symptoms arising from ARR infection, which remains a perennial bottleneck to the successful evaluation and incorporation of disease resistance into new cultivars. In this study, we developed a greenhouse-based high throughput phenotyping (HTP) platform that moves along the rails above the greenhouse benches and captures the visual symptoms caused byAphanomyces euteichesin field pea. We pilot tested this platform alongside with conventional visual scoring in five experimental trials under greenhouse conditions, assaying over 12,600 single plants. Precision estimated through broad-sense heritability (H2) was consistently higher for the HTP-indices (H2Exg =0.86) than the traditional visual scores (H2DSI=0.59), potentially increasing the power of genetic mapping. We genetically dissected variation for ARR resistance using the HTP-indices, and identified a total of 260 associated single nucleotide polymorphism (SNP) through genome-wide association (GWA) mapping. The number of associated SNP for HTP-indices was consistently higher with some SNP overlapped to the associated SNP identified using the visual scores. We identified numerous small-effect QTLs, with the most significant SNP explaining about 5 to 9% of the phenotypic variance per index, and identified previously mapped genes known to be involved in the biological pathways that trigger immunity against ARR, including Psat5g280480, Psat5g282800, Psat5g282880, and Psat2g167800. We also identified a few novel QTLs with small-effect sizes that may be worthy of validation in the future. The newly identified QTLs and underlying genes, along with genotypes with promising resistance identified in this study, can be useful for improving a long-term, durable resistance to ARR.
Rapid and accurate assembly of large DNA assisted by in vitro packaging of bacteriophage
Authors: Nozaki Shingo 
Published: August 2022

AbstractDevelopment of DNA assembly methods made it possible to construct large DNA. However, achieving the large DNA assembly easily, accurately, and at low cost remains a challenge. This study shows that DNA assembled only by annealing of overlapping single-stranded DNA ends, which are generated by exonuclease treatment, without ligation can be packaged in phage particles and can also be transduced into bacterial cells. Based on this, I developed a simple method to construct long DNA of about 40 - 50 kb from multiple PCR fragments using the bacteriophage in vitro packaging system. This method, named iPac (in vitroPackaging-assisted DNA assembly), allowed accurate and rapid construction of large plasmids and phage genomes. This simple method will accelerate research in molecular and synthetic biology, including the construction of gene circuits or the engineering of metabolic pathways.Abstract Figure
Left anterior fascicular block is associated with non-ischemic myocardial scar and proportionately decreased ejection fraction
Authors: Scheele Johan von , Atwater Brett D , Klem Igor , Engblom Henrik , Loewenstein Daniel E , Wieslander Björn , Ugander Martin 
Published: August 2022

AbstractBackgroundLeft anterior fascicular block (LAFB) has been associated with increased mortality, but the underlying causes are unknown.ObjectivesTo determine whether LAFB is associated with increased left ventricular (LV) scar burden and reduced LV ejection fraction (LVEF).MethodsLAFB patients (n=51) and matched control patients (n=600) were retrospectively enrolled. Both groups had been referred for cardiovascular magnetic resonance imaging (CMR) and electrocardiography (ECG). They were compared regarding size and location of LV scar, LVEF, and a dysfunction index describing the difference between measured LVEF and expected LVEF based on scar size.ResultsPatients with LAFB had on average a larger LV scar (median [interquartile range] 0.7 [0.0-6.6] vs 0.0 [0.0-1.5] % LV mass, p<0.001). LAFB was associated with a higher prevalence of any scar (59% vs 33%, p<0.001). The groups had similar prevalence of ischemic scar (29% vs 23%, p=0.40) but LAFB patients a higher prevalence of non-ischemic scar (29% vs 10%, p=0.001) most frequently located in the basal and mid inferoseptal segments and the anterior and lateral apical LV segments. LVEF was lower in LAFB than in controls (58 [43-60] vs 60 [55-60] %, p=0.02). There was no difference in dysfunction index (24.0 [17.8-25.5] vs 24.0 [19.0-27.8] %-points of LVEF, p=0.32).ConclusionsIn a matched cohort, LAFB was associated with a small decrease in LVEF that was proportionate to the increased LV scar burden, which was more commonly of non-ischemic etiology and not infarction, and not more commonly located near the expected course of the left anterior fascicle.