bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heatrich-BS enables efficient CpG enrichment and highly scalable cell-free DNA methylation profiling
Authors: Cheruba Elsie , Viswanathan Ramya , Wong Pui-Mun , Womersley Howard John , Lau Yiting , Gan Anna , Poon Polly S.Y. , Ng Sarah B. , Chong Dawn Qingqing , Tan Iain Beehuat , Cheow Lih Feng 
Published: April 2021

AbstractGenome wide analysis of cell-free DNA (cfDNA) methylation profile has been shown to be a promising approach for sensitive and specific multi-cancer detection. However, scaling these assays for clinical translation is impractical due to the high cost of whole genome bisulfite sequencing. We showed that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbored the majority of cancer-specific methylation signature. Here, we report on the simple but effective Heat enrichment of CpG-rich regions for Bisulfite Sequencing (Heatrich-BS) platform that enables focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable high accuracy and sensitivity in tumor burden estimation and quantitative monitoring of colorectal patient response to treatment, at much reduced sequencing requirement. Heatrich-BS holds great potential for highly scalable screening and regular monitoring of cancer using liquid biopsy.
Cerebello-Basal Ganglia Networks and Cortical Network Global Efficiency
Authors: Jackson T. Bryan , Bernard Jessica A. 
Published: April 2021

AbstractThe cerebellum (CB) and basal ganglia (BG) each have topographically distinct functional subregions that are functionally and anatomically interconnected with cortical regions through discrete thalamic loops and with each other via disynaptic connections, with previous work detailing high levels of functional connectivity between these phylogenetically ancient regions. It was posited that this CB-BG network provides support for cortical systems processing, spanning cognitive, emotional, and motor domains, implying subcortical network measures are strongly related to cortical network measures (Bostan & Strick, 2018); however, it is currently unknown how network measures within distinct CB-BG networks relate to cortical network measures. Here, 122 regions of interest comprising cognitive and motor CB-BG networks and 7 canonical cortical resting-state were used to investigate whether the integration (quantified using global efficiency, GE) of cognitive CB-BG network (CCBN) nodes and their segregation from motor CB-BG network (MCBN) nodes is related to cortical network GE and segregation in 233 non-related, right- handed participants (Human Connectome Project-1200). CCBN GE positively correlated with GE in the default mode, motor, and auditory networks and MCBN GE positively correlated with GE in all networks except the default mode and emotional. MCBN segregation was related to MN segregation. These findings highlight the CB-BG network’s role in executive function, task switching, and verbal working memory. This work has implications for understanding cortical network organization and cortical-subcortical interactions in healthy adults and may help in deciphering subcortical differences seen in disease states.
Optimizing touchscreen measures of rodent cognition by eliminating image bias
Authors: Belarde James A. , Chen Claire W. , Rafikian Elizabeth , Yang Mu , Troy Carol M. 
Published: April 2021

ABSTRACTFor the last twenty years, the Bussey-Saksida touchscreen-based operant conditioning platform has evolved in close parallel alongside the Cambridge Neuropsychological Test Automated Battery (CANTAB) to produce batteries of tests for studying complex cognitive functions in rodents that are increasingly analogous to human diagnostic tests and greatly narrow the translational gap in cognition research. Naturally, with this increasing usefulness comes increasing use, particularly by non-experts. This necessitates a greater understanding of, and a better controlling for, confounding factors that may limit the system’s ability to optimally detect cognitive deficits when used as a widely accessible and commercially available standardized task. In the present study, we show a strong image preference bias in a standard pairwise discrimination task with a widely used spider-plane image pairing in a putative animal model for intellectual disability. This bias greatly influenced the performance of our experimental mice, significantly affecting the length of time it took mice to complete the task, their progress over time, and several accessory measures usefully recorded by the Bussey-Saksida touchscreen system. We further show that this bias can be corrected by using more similar image pairings without sacrificing the animal’s ability to learn to distinguish the stimuli. This approach eliminated all significant stimuli specific differences seen with the spider-plane pairing. We then analyzed the pixel composition of the various stimuli to suggest that the bias is due to a difference in image brightness. These findings highlight the importance of carefully modulating paired touchscreen stimuli to ensure equivalence prior to learning and the need for more studies of visual perception in mice, particularly as it relates to their performance in cognitive assays.
Modeling the role of mortality-based response triggers on the effectiveness of African swine fever control strategies
Authors: Machado Gustavo , Farthing Trevor , Andraud Mathieu , Lopes Francisco Paulo Nunes , Lanzas Cristina 
Published: April 2021

African swine fever (ASF) is considered the most impactful transboundary swine disease. In the absence of effective vaccines, control strategies are heavily dependent on mass depopulation and movement restrictions. Here we developed a nested multiscale model for the transmission of ASF, combining spatially explicit network model of animal movements with a deterministic compartmental model for the dynamics of two ASF strains within-pixels of 3 km x 3 km, amongst the pig population in one Brazilian state. The model outcomes are epidemic duration, number of secondary infected farms and pigs, and distance of ASF spread. The model also shows the spatial distribution of ASF epidemics. We analyzed quarantine-based control interventions in the context of mortality trigger thresholds for the deployment of control strategies.The mean epidemic duration of a moderately virulent strain was 11.2 days assuming the first infection is detected (best-case scenario) and 15.9 days when detection is triggered at 10 % mortality. For a highly virulent strain, the epidemic duration was 6.5 days and 13.1 days, respectively. The distance from the source to infected locations and the spatial distribution was not dependent on strain virulence. Under the best-case scenario, we projected an average number of infected farms of 23.77 farms and 18.8 farms for the moderate and highly virulent strains, respectively. At 10% mortality-trigger, the predicted number of infected farms was on average 46.27 farms and 42.96 farms, respectively. We also demonstrated that the establishment of ring quarantine zones regardless of size (i.e., 5 km, 15 km) was outperformed by backward animal movement tracking. The proposed modeling framework provides an evaluation of ASF epidemic potential, providing a ranking of quarantine-based control strategies that could assist animal health authorities in planning the national preparedness and response plan.
Synapse development is regulated by microglial THIK-1 K+channels
Authors: Izquierdo Pablo , Shiina Hiroko , Hirunpattarasilp Chanawee , Sethi Huma , Attwell David 
Published: April 2021

ABSTRACTMicroglia are the resident immune cells of the central nervous system. They constantly survey the brain parenchyma for redundant synapses, debris or dying cells, which they remove through phagocytosis. Microglial ramification, motility and cytokine release are regulated by tonically active THIK-1 K+channels on the microglial plasma membrane. Here, we examined whether these channels play a role in phagocytosis. Using pharmacological blockers and THIK-1 knockout (KO) mice, we found that lack of THIK-1 activity reduced microglial phagocytosis, which may result in impaired pruning of synapses. In hippocampus, mice lacking THIK-1 expression had an increased number of glutamatergic synapses during development. This resulted from an increased number of presynaptic terminals, due to impaired removal by THIK-1 KO microglia. In microglia in brain slices from fresh human biopsies, modulating THIK-1 function had effects similar to those in rodents: blocking THIK-1 rapidly reduced microglial process ramification and increased synaptic density. The dependence of synapse number on THIK-1 K+channels, which control microglial surveillance and phagocytic ability, implies that changes in THIK-1 expression level over the lifespan or in disease states may contribute to altering neural circuit function.SignificanceMicroglia are the brain’s resident immune cells, surveying it with motile processes, which can remove pathogens but also prune unnecessary junctions between the neurons (synapses). A potassium channel, THIK-1, in the microglial membrane allows efflux of potassium from these cells, and thereby regulates their membrane voltage as well as their process motility and release of inflammatory mediators. Here, using THIK-1-blocking drugs and THIK-1-deficient mice, we demonstrate that THIK-1 controls removal of synaptic material by microglia, which reduces the number of functional synapses. We also show that blocking THIK-1, as some anaesthetics do, affects microglial structure and increases the number of synapses in living brain slices from both rodents and humans, and could thus alter network function in the brain.
Large-scale voltage imaging in the brain using targeted illumination
Authors: Xiao Sheng , Lowet Eric , Gritton Howard J. , Fabris Pierre , Wang Yangyang , Sherman Jack , Mount Rebecca , Tseng Hua-an , Man Heng-Ye , Mertz Jerome , Han Xue 
Published: April 2021

AbstractRecent improvements in genetically encoded voltage indicators enabled optical imaging of action potentials and subthreshold membrane voltage dynamics from single neurons in the mammalian brain. To perform high speed voltage imaging, widefield microscopy remains an essential tool for recording activity from many neurons simultaneously over a large anatomical area. However, the lack of optical sectioning makes widefield microscopy more prone to background signal contamination, and thus far voltage imaging using fully genetically encoded voltage indicators remains limited to simultaneous sampling of a few cells over a restricted field-of-view. We here demonstrate a strategy for large scale voltage imaging using the fully genetically encoded voltage indicator SomArchon and targeted illumination. We implemented a simple, low-cost digital micromirror device based targeted illumination strategy to restrict illumination to the cells of interest, and systematically quantified the improvement of this microscopy design theoretically and experimentally with SomArchon expressing neurons in single layer cell cultures and in the brains of awake mice. We found that targeted illumination, in comparison to widefield illumination, increased SomArchon signal contrast and reduced background cross-contamination in the brain. Such improvement permitted the reduction of illumination intensity, and thus reduced fluorescence photobleaching and prolonged imaging duration. When coupled with a high-speed, large area sCMOS camera, we routinely imaged tens of spiking neurons simultaneously over minutes in the brain. Thus, the widefield microscopy design with an integrated targeted illumination system described here offers a simple solution for voltage imaging analysis of large neuron populations in behaving animals.
ECNano: A Cost-Effective Workflow for Target Enrichment Sequencing and Accurate Variant Calling on 4,800 Clinically Significant Genes Using a Single MinION Flowcell
Authors: Leung Amy Wing-Sze , Leung Henry Chi-Ming , Wong Chak-Lim , Zheng Zhen-Xian , Lui Wui-Wang , Luk Ho-Ming , Lo Ivan Fai-Man , Luo Ruibang , Lam Tak-Wah 
Published: April 2021

AbstractBackgroundThe application of long-read sequencing using the Oxford Nanopore Technologies (ONT) MinION sequencer is getting more diverse in the medical field. Having a high sequencing error of ONT and limited throughput from a single MinION flowcell, however, limits its applicability for accurate variant detection. Medical exome sequencing (MES) targets clinically significant exon regions, allowing rapid and comprehensive screening of pathogenic variants. By applying MES with MinION sequencing, the technology can achieve a more uniform capture of the target regions, shorter turnaround time, and lower sequencing cost per sample.MethodWe introduced a cost-effective optimized workflow, ECNano, comprising a wet-lab protocol and bioinformatics analysis, for accurate variant detection at 4,800 clinically important genes and regions using a single MinION flowcell. The ECNano wet-lab protocol was optimized to perform long-read target enrichment and ONT library preparation to stably generate high-quality MES data with adequate coverage. The subsequent variant-calling workflow, Clair-ensemble, adopted a fast RNN-based variant caller, Clair, and was optimized for target enrichment data. To evaluate its performance and practicality, ECNano was tested on both reference DNA samples and patient samples.ResultsECNano achieved deep on-target depth of coverage (DoC) at average >100x and >98% uniformity using one MinION flowcell. For accurate ONT variant calling, the generated reads sufficiently covered 98.9% of pathogenic positions listed in ClinVar, with 98.96% having at least 30x DoC. ECNano obtained an average read length of 1,000 bp. The long reads of ECNano also covered the adjacent splice sites well, with 98.5% of positions having ≥ 30x DoC. Clair-ensemble achieved >99% recall and accuracy for SNV calling. The whole workflow from wet-lab protocol to variant detection was completed within three days.ConclusionWe presented ECNano, an out-of-the-box workflow comprising (1) a wet-lab protocol for ONT target enrichment sequencing and (2) a downstream variant detection workflow, Clair-ensemble. The workflow is cost-effective, with a short turnaround time for high accuracy variant calling in 4,800 clinically significant genes and regions using a single MinION flowcell. The long-read exon captured data has potential for further development, promoting the application of long-read sequencing in personalized disease treatment and risk prediction.
Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters
Authors: Saleh Moustafa M. , Jeronimo Célia , Robert François , Zentner Gabriel E. 
Published: April 2021

AbstractThe Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels of PIC formation at SAGA-requiring and TFIID-dependent genes. We suggest that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.
Linking null models to hypotheses to improve nestedness analysis
Authors: Pereira Pinheiro Rafael Barros , Dormann Carsten F. , Félix Ferreira Gabriel Moreira , Ribeiro Mello Marco Aurelio 
Published: April 2021

ABSTRACTNestedness is a common pattern in metacommunities and interaction networks, whose causes are still subject to investigation. Nestedness inference is challenging because, beyond calculating an index, we need to compare observed and expected values using null models. There are many different null models and the choice between them strongly affects test outcomes. Furthermore, there is no theoretical basis to guide this choice.Here, we propose a different look at the meaning of nestedness that improves our understanding of its causes and directly links null models to hypotheses. The nestedness of a matrix is the combination of marginal sum inequality and high overlap. The higher the overlap, the more predictable the cell values by marginal sums. Therefore, the only way a process can increase nestedness is by promoting marginal sum inequalities, without concomitantly introducing preferences. We propose a combination of null models to test for different topological hypotheses. In these null models, interactions are randomized following a probability matrix. The probability matrix of the equiprobable model excludes marginal sum inequalities and consequently all nestedness-generating mechanisms, providing a distribution of expected values for nestedness significance tests. The probability matrix of the proportional model, by conserving marginal sums and maximizing overlap, conserves nestedness-generating mechanisms and excludes nestedness-disrupting mechanisms, thereby yielding the expected nestedness values for fully nested matrices.We advance a new protocol to test for nestedness in binary and weighted matrices, in which those two null models represent different topological hypotheses. Our protocol helps to tell apart cases in which nestedness is different from expected by chance and cases in which nestedness represents the best topological archetype. We also evaluate the efficiency of applying this protocol using some common nestedness indices. Analyses based on weighted data proved to be highly efficient and informative, while binary analyses induced severe distortions. Finally, we empirically illustrate our approach using a plant-pollinator network.Through a shift of perspective, our approach reconciliates contradictions in null model analysis and provides a guideline for nestedness interpretation.
Novel antiviral interferon sensitive genes unveiled by correlation-driven gene selection and integrated systems biology approaches
Authors: Cheroni Cristina , Manganaro Lara , Donnici Lorena , Bevilacqua Valeria , Bonnal Raoul J.P. , Rossi Riccardo L. , De Francesco Raffaele 
Published: April 2021

AbstractInterferons (IFNs) are key cytokines involved in alerting the immune system to viral infection. After IFN stimulation, cellular transcriptional profile critically changes, leading to the expression of several IFN stimulated genes (ISGs) that exert a wide variety of antiviral activities. Despite many ISGs have been already identified, a comprehensive network of coding and non-coding genes with a central role in IFN-response still needs to be elucidated. We performed a global RNA-Seq transcriptome profile of the HCV permissive human hepatoma cell line Huh7.5 and its parental cell line Huh7, upon IFN treatment, to define a network of genes whose coordinated modulation plays a central role in IFN-response. Our study adds molecular actors, coding and non-coding genes, to the complex molecular network underlying IFN-response and shows how systems biology approaches, such as correlation networks, network’s topology and gene ontology analyses can be leveraged to this aim.
R-SPONDIN2+Mesenchymal Cells Form the Bud Tip Progenitor Niche During Human Lung Development
Authors: Hein Renee F.C. , Wu Joshua H. , Tsai Yu-Hwai , Wu Angeline , Miller Alyssa J. , Holloway Emily M. , Frum Tristan , Conchola Ansley S. , Szenker-Ravi Emmanuelle , Reversade Bruno , Yan Kelley S. , Kuo Calvin J. , Spence Jason R. 
Published: April 2021

SUMMARYMammalian respiratory system development is regulated by complex reciprocal signaling events that take place between epithelial cells and the surrounding mesenchymal cells; however, mesenchymal heterogeneity and function in the developing human lung is poorly understood. We interrogated single cell RNA sequencing data from multiple human lung specimens and identified a mesenchymal cell population present during development that is highly enriched for expression of the WNT agonistR-SPONDIN2(RSPO2), and we found that adjacent epithelial bud tip progenitors are enriched for the RSPO2 receptorLGR5. By carrying out functional experiments using organoid models, lung explant cultures, and FACS-isolatedRSPO2+mesenchyme, we show that RSPO2 is a critical niche cue that potentiates WNT signaling in human lung progenitors to maintain their multipotency.
Species-specific gene duplication inArabidopsis thalianaevolved novel phenotypic effects on morphological traits under strong positive selection
Authors: Huang Yuan , Chen Jiahui , Dong Chuan , Sosa Dylan , Xia Shengqian , Ouyang Yidan , Fan Chuanzhu , Li Dezhu , Mortola Emily , Long Manyuan , Bergelson Joy 
Published: April 2021

AbstractGene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, the ways in which new duplicate genes contribute to phenotypic evolution remain largely unknown, especially in plants, owing to a lack of experimental and phenotypic data. In this study, we identified the new geneExov,derived from a partial gene region duplication of its parental geneExov-L, which is a member of an exonuclease family, into a different chromosome inArabidopsis thaliana. We experimentally investigated the phenotypic effects ofExovandExov-Lin an attempt to understand how the new gene diverged from the parental copy and contributes to phenotypic evolution. Evolutionary analysis demonstrated thatExovis a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNAseq analyses reveal that the new gene, despite its young age, has acquired a large number of novel direct and indirect interactions in which the parental gene does not engage. This is consistent with a high, selection-driven substitution rate in the protein sequence encoded byExovin contrast to the slowly evolvingExov-L, suggesting an important role forExovin phenotypic evolution. We analyzed phenotypic effects ofexovandexov-lsingle T-DNA-insertion mutants;doubleexov, exov-lT-DNA insertion mutants; and CRISPR/Cas9-mediatedexovcrpandexov-lcrpknockouts on seven morphological traits in both the new and parental genes. We detected significant segregation of morphological changes for all seven traits when assessed in terms of single mutants, as well as morphological changes for seven traits associated with segregation of doubleexov, exov-lmutants. Substantial divergence of phenotypic effects between new and parental genes was revealed by principal component analyses, suggesting neofunctionalization in the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological and developmental evolution inArabidopsis thaliana.