bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computed Tomography Features of COVID-19 in Children: A Systematic Review and Meta-analysis
Authors: Wang Ji-gan , Mo Yu-fang , Su Yu-heng , Wang Li-chuang , Liu Guang-bing , Meng-Li  , Qin Qian-qiu 
Published: September 2020

AbstractObjectivesTo systematically analyze the chest CT imaging features of children with COVID-19 and provide references for clinical practice.MethodsWe searched PubMed, Web of Science, and Embase; data published by Johns Hopkins University; and Chinese databases CNKI, Wanfang, and Chongqing Weipu. Reports on chest CT imaging features of children with COVID-19 from January 1, 2020, to August 10, 2020, were analyzed retrospectively and a meta-analysis carried out using Stata12.0 software.ResultsThirty-seven articles (1747 children) were included in this study. The overall rate of abnormal lung CT findings was 63.2% (95% confidence interval [CI]: 55.8–70.6%), with a rate of 61.0% (95% CI: 50.8–71.2%) in China and 67.8% (95% CI: 57.1–78.4%) in the rest of the world in the subgroup analysis. The incidence of ground-glass opacities was 39.5% (95% CI: 30.7–48.3%), multiple lung lobe lesions 65.1% (95% CI: 55.1–67.9%), and bilateral lung lesions 61.5% (95% CI: 58.8–72.2%). Other imaging features included nodules (25.7%), patchy shadows (36.8%), halo sign(24.8%), consolidation (24.1%), air bronchogram signs (11.2%), cord-like shadows (9.7%), crazy-paving pattern (6.1%), and pleural effusion (9.1%). Two articles reported three cases of white lung, another reported two cases of pneumothorax, and another one case of bullae.CONCLUSIONThe lung CT results of children with COVID-19 are usually normal or slightly atypica, with a low sensitivity and specificity compared with that in adults. The lung lesions of COVID-19 pediatric patients mostly involve both lungs or multiple lobes, and the common manifestations are patchy shadows, ground-glass opacities, consolidation, partial air bronchogram signs, nodules, and halo signs; white lung, pleural effusion, and paving stone signs are rare.CLINICAL IMPACTTherefore, chest CT has limited value as a screening tool for children with COVID-19 and can only be used as an auxiliary assessment tool.RegistrationThis systematic review and meta-analysis was registered in the Prospero International Prospective Register of Systemic Reviews (CRD42020196602).Strengths and limitations of this studyThe lung CT findings of children with COVID-19 are usually normal or slightly atypical, with a low sensitivity and specificity compared with that in adults. From a systematic review of current literature, the overall rate of abnormal lung CT findings in children was revealed to be 63.2%.Chest CT has limited value as a screening tool for children with COVID-19 and can only be used as an auxiliary assessment tool.The sample size of some included studies is small, which may affect the results.
Isolation of potential plant growth-promoting bacteria from nodules of legumes grown in arid Botswana soil
Authors: Kosty Melissa , Pule-Meulenberg Flora , Humm Ethan A. , Martínez-Hidalgo Pilar , Maymon Maskit , Mohammadi Sophia , Cary Josh , Yang Paul , Reddi Krisanavane , Huntemann Marcel , Clum Alicia , Foster Brian , Foster Bryce , Roux Simon , Palaniappan Krishnaveni , Varghese Neha , Mukherjee Supratim , Reddy T.B.K. , Daum Chris , Copeland Alex , Ivanova Natalia N. , Kyrpides Nikos C. , del Rio Tajana Glavina , Eloe-Fadrosh Emiley A. , Hirsch Ann M. 
Published: September 2020

AbstractAs the world population increases, improvements in crop growth and yield will be needed to meet rising food demands, especially in countries that have not developed agricultural practices optimized for their own soils and crops. In many African countries, farmers improve agricultural productivity by applying synthetic fertilizers and pesticides to crops, but their continued use over the years has had serious environmental consequences including air and water pollution as well as loss of soil fertility. To reduce the overuse of synthetic amendments, we are developing inocula for crops that are based on indigenous soil microbes, especially those that enhance plant growth and improve agricultural productivity in a sustainable manner. We first isolated environmental DNA from soil samples collected from an agricultural region to study the composition of the soil microbiomes and then used Vigna unguiculata (cowpea), an important legume crop in Botswana and other legumes as “trap” plants using the collected soil to induce nitrogen-fixing nodule formation. We have identified drought-tolerant bacteria from Botswana soils that stimulate plant growth; many are species of Bacillus and Paenibacillus. In contrast, the cowpea nodule microbiomes from plants grown in these soils house mainly rhizobia particularly Bradyrhizobium, but also Methylobacterium spp. Hence, the nodule microbiome is much more limited in non-rhizobial diversity compared to the soil microbiome, but also contains a number of potential pathogenic bacteria.
miR-200deficiency promotes lung cancer metastasis by activating cancer-associated fibroblasts
Authors: Xue Bin , Chuang Chen-Hua , Prosser Haydn M. , Fuziwara Cesar Seigi , Chan Claudia , Sahasrabudhe Neil , Kühn Maximilian , Wu Yalei , Chen Jingqi , Biton Anne , Chen Caifu , Wilkinson John Erby , McManus Michael T. , Bradley Allan , Winslow Monte M , Su Bo , He Lin 
Published: September 2020

AbstractLung adenocarcinoma, the most prevalent lung cancer subtype, is characterized by its high propensity to metastasize. Despite the importance of metastasis in lung cancer mortality, its underlying cellular and molecular mechanisms remain largely elusive. Here, we identifiedmiR-200miRNAs as potent suppressors for lung adenocarcinoma metastasis.miR-200expression is specifically repressed in mouse metastatic lung adenocarcinomas, andmiR-200decrease strongly correlates with poor patient survival. Consistently, deletion ofmir-200c/141in theKrasLSL-G12D/+; Trp53flox/floxlung adenocarcinoma mouse model significantly promoted metastasis, generating a desmoplastic tumor stroma highly reminiscent of metastatic human lung cancer.miR-200deficiency in lung cancer cells promotes the proliferation and activation of adjacent cancer-associated fibroblasts (CAFs), which in turn elevates the metastatic potential of cancer cells.miR-200regulates the functional interaction between cancer cells and CAFs, at least in part, by targeting Notch ligand Jagged1 and Jagged2 in cancer cells and inducing Notch activation in adjacent CAFs. Hence, the interaction between cancer cells and CAFs constitutes an essential mechanism to promote metastatic potential.
Graph Convolutional Network-based Method for Clustering Single-cell RNA-seq Data
Authors: Zeng Yuansong , Lin Jinxing , Zhou Xiang , Lu Yutong , Yang Yuedong 
Published: September 2020

AbstractSingle-cell RNA sequencing (scRNA-seq) technologies promise to characterize the transcriptome of genes at cellular resolution, which shed light on unfolding cell heterogeneity and diversity. Fast-growing scRNA-seq profiles require efficient clustering algorithms to identify the same type of cells. Although many methods have been developed for cell clustering, existing clustering methods are limited to extract the representations from expression data of individual cells, while ignoring the high-order structural relations between cells. Here, we proposed GraphSCC, a robust graph artificial intelligence model to cluster single cells by accounting for structural relations between cells. The representation learned from the graph convolutional network, together with another representation output from a denoising autoencoder network, are optimized by a dual self-supervised module for better cell clustering. The experimental results indicate that GraphSCC model outperforms state-of-the-art methods in terms of various evaluation metrics on both simulated and real datasets. Further visualizations show that GraphSCC provides representations for better intra-cluster compactness and inter-cluster separability.
C/EBPβ regulates hypertrophic versus hyperplastic fat tissue growth
Authors: Müller Christine , Zidek Laura M. , Eichwald Sabrina , Calkhoven Cornelis F. 
Published: September 2020

AbstractChronic obesity is correlated with severe metabolic and cardiovascular diseases as well as with an increased risk for developing cancers. Obesity is usually characterized by fat accumulation in enlarged - hypertrophic – adipocytes that are a source of inflammatory mediators, which is seen as causal for developing metabolic disorders. Yet, in certain healthy obese individuals fat is stored in metabolically more favorablehyperplasticfat tissue that contains an increased number of smaller adipocytes that are less inflamed. In a previous study we demonstrated that C/EBPβ-LIP deficient, yet C/EBPβ-LAP proficient mice show an expanded health and lifespan. Here we show that in mice on a high-fat diet LIP-deficiency results in adipocyte hyperplasia as well as efficient fat storage in subcutaneous depots associated with metabolic and inflammatory improvements. Our data identify C/EBPβ as a regulator of adipocyte fate in response to increased fat intake, which has major implications for metabolic health and aging.
comboFM: leveraging multi-way interactions for systematic prediction of drug combination effects
Authors: Julkunen Heli , Cichonska Anna , Gautam Prson , Szedmak Sandor , Douat Jane , Pahikkala Tapio , Aittokallio Tero , Rousu Juho 
Published: September 2020

AbstractWe presentcomboFM, a machine learning framework for predicting the responses of drug combinations in preclinical studies, such as those based on cell lines or patient-derived cells.comboFMmodels the cell context-specific drug interactions through higher-order tensors, and efficiently learns latent factors of the tensor using powerful factorization machines. The approach enablescomboFMto leverage information from previous experiments performed on similar drugs and cells when predicting responses of new combinations in so far untested cells; thereby, it achieves highly accurate predictions despite sparsely populated data tensors. We demonstrated high predictive performance ofcomboFMin various prediction scenarios using data from cancer cell line drug screening. Subsequent experimental validation of a set of previously untested drug combinations further supported the practical and robust applicability ofcomboFM. For instance, we confirmed a novel synergy between anaplastic lymphoma kinase (ALK) inhibitor crizotinib and proteasome inhibitor bortezomib in lymphoma cells. Overall, our results demonstrate thatcomboFMprovides an effective means for systematic pre-screening of drug combinations to support precision oncology applications.
ETV7 regulates breast cancer stem-like cell plasticity by repressing IFN-response genes
Authors: Pezzè Laura , Forcato Mattia , Pontalti Stefano , Badowska Kalina Aleksandra , Rizzotto Dario , Skvortsova Ira-Ida , Bicciato Silvio , Ciribilli Yari 
Published: September 2020

ABSTRACTCancer stem cells (CSCs) represent a population of cells within the tumor able to drive tumorigenesis and known to be highly resistant to conventional chemotherapy and radiotherapy. In this work, we show a new role for ETV7, a transcriptional repressor member of the ETS family, in promoting breast cancer stem-like cells plasticity and resistance to chemo- and radiotherapy in breast cancer (BC) cells. We observed that MCF7 and T47D BC-derived cells stably over-expressing ETV7 showed reduced sensitivity to the chemotherapeutic drug 5-Flouororuacil and to radiotherapy, accompanied by an adaptive proliferative behavior observed in different culture conditions. We further noticed that alteration of ETV7 expression could significantly affect the population of breast CSCs, measured by CD44+/CD24lowcell population and mammosphere formation efficiency. By transcriptome profiling, we identified a signature of Interferon-responsive genes significantly repressed in cells over-expressing ETV7, which could be responsible for the increase in the breast CSCs population, as this could be partially reverted by the treatment with IFN-β. Lastly, we show that the expression of the IFN-responsive genes repressed by ETV7 could have prognostic value in breast cancer, as low expression of these genes was associated with a worse prognosis. Therefore, we propose a novel role for ETV7 in breast cancer stem cells’ plasticity and associated resistance to conventional chemotherapy and radiotherapy, which involves the repression of a group of IFN-responsive genes, potentially reversible upon IFN-β treatment. We, therefore, suggest that an in-depth investigation of this mechanism could lead to novel breast CSCs targeted therapies and to the improvement of combinatorial regimens, possibly involving the therapeutic use of IFN-β, with the aim of avoiding resistance development and relapse in breast cancer.
CRISPR-nRAGE, a Cas9 nickase-reverse transcriptase assisted versatile genetic engineering toolkit forE. coli
Authors: Tong Yaojun , Jørgensen Tue S. , Whitford Christopher M. , Weber Tilmann , Lee Sang Yup 
Published: September 2020

AbstractIn most prokaryotes, missing and poorly active non-homologous end joining (NHEJ) DNA repair pathways heavily restrict the direct application of CRISPR-Cas for DNA double-strand break (DSB)-based genome engineering without providing editing templates. CRISPR base editors, on the other hand, can be directly used for genome engineering in a number of bacteria, includingE. coli, showing advantages over CRISPR-Cas9, since they do not require DSBs. However, as the current CRISPR base editors can only engineer DNA by A to G or C to T/G/A substitutions, they are incapable of mediating deletions, insertions, and combinations of deletions, insertions and substitutions. To address these challenges, we developed a Cas9 nickase (Cas9n)-reverse transcriptase (Moloney Murine Leukemia Virus, M-MLV) mediated, DSB-free, versatile, and single-nucleotide resolution genetic manipulation toolkit for prokaryotes, termed CRISPR-nRAGE (CRISPR-Cas9n Reverse transcriptase Assisted Genome Engineering) system. CRISPR-nRAGE can be used to introduce substitutions, deletions, insertions, and the combination thereof, both in plasmids and the chromosome ofE. coli. Notably, small sized-deletion shows better editing efficiency compared to other kinds of DNA engineering. CRISPR-nRAGE has been used to delete and insert DNA fragments up to 97 bp and 33 bp, respectively. Efficiencies, however, drop sharply with the increase of the fragment size. It is not only a useful addition to the genome engineering arsenal forE. coli, but also may be the basis for the development of similar toolkits for other organisms.
Peroxisomes contribute to intracellular calcium dynamics
Authors: Sargsyan Yelena , Bickmeyer Uta , Streckfuss-Bömeke Katrin , Bogeski Ivan , Thoms Sven 
Published: September 2020

AbstractPeroxisomes communicate with other cellular compartments by transfer of various metabolites. However, whether peroxisomes are sites for calcium handling and exchange has remained contentious. Here we generated sensors for assessment of peroxisomal calcium and applied them for single cell-based calcium imaging in HeLa cells and cardiomyocytes. We found that peroxisomes in HeLa cells take up calcium upon depletion of intracellular calcium stores and upon calcium influx across the plasma membrane. Further, we show that peroxisomes of neonatal rat cardiomyocytes and human induced pluripotent stem cell-derived cardiomyocytes can take up calcium in a controlled manner. Our results indicate that peroxisomal and cytosolic calcium signals are tightly interconnected. Hence, peroxisomes may play an important role in shaping cellular calcium dynamics by serving as buffers or sources of intracellular calcium.
Human-associated microbiota suppress invading bacteria even under disruption by antibiotics
Authors: Letten Andrew D. , Baumgartner Michael , Pfrunder-Cardozo Katia R. , Levine Jonathan , Hall Alex R. 
Published: September 2020

AbstractIn light of their adverse impacts on resident microbial communities, it is widely predicted that broad-spectrum antibiotics can promote the spread of resistance by releasing resistant strains from competition with other strains and species. We investigated the invasion success of a resistant strain ofEscherichia coliinoculated into human-associated communities in the presence and absence of the broad and narrow spectrum antibiotics rifampicin and polymyxin B, respectively. We found strong evidence of community-level suppression of the resistant strain in the absence of antibiotics and, despite large changes in community composition and abundance following rifampicin exposure, suppression of the invading resistant strain was maintained in both antibiotic treatments. Instead, the strength of competitive suppression was more strongly associated with the individual donor from which the community was sampled. This suggests microbiome composition strongly influences susceptibility to invasion by antibiotic-resistant strains, but at least some antibiotic-associated disruption can be tolerated before invasion susceptibility increases. A deeper understanding of this association will aid the development of ecologically-aware strategies for managing antibiotic resistance.
Phenotypic and transcriptomic responses to stress differ according to population geography in an invasive species
Authors: Marin Pierre , Jaquet Angelo , Picarle Justine , Fablet Marie , Merel Vincent , Delignette-Muller Marie-Laure , Ferrarini Mariana Galvão , Gibert Patricia , Vieira Cristina 
Published: September 2020

AbstractBackgroundAdaptation to rapid environmental changes must occur within a short time scale. In this context, studies of invasive species may provide insights into the underlying mechanisms of rapid adaptation as these species have repeatedly encountered and successfully adapted to novel environmental conditions. Here we investigated how invasive and non-invasive populations ofD. suzukiideal with an oxidative stress at both the phenotypic and molecular level. We also investigated the impact of transposable element insertions on the differential gene expression between genotypes in response to oxidative stress.ResultsInvasive populations lived longer in the untreated condition than non-invasive Japanese populations. As expected, lifespan was greatly reduced following exposure to paraquat, but this reduction varied among genotypes (a genotype by environment interaction, GEI) with invasive genotypes appearing more affected by exposure than non-invasive genotypes. We also performed transcriptomic sequencing of selected genotypes upon and without paraquat and detected a large number of genes differentially expressed, distinguishing the genotypes in the untreated environment. While a small core set of genes were differentially expressed by all genotypes following paraquat exposure, much of the response of each population was unique. Interestingly, we identified a set of genes presenting genotype by environment interaction (GEI). Many of these differences may reflect signatures of history of past adaptation. Transposable elements (TEs) were not activated after oxidative stress and differentially expressed (DE) genes were significantly depleted of TEs.ConclusionIn the decade since the invasion from the south of Asia, invasive populations ofD. suzukiihave diverged from populations in the native area regarding their genetic response to oxidative stress. This suggests that such transcriptomic changes could be involved in the rapid adaptation to local environments.
Graphia: A platform for the graph-based visualisation and analysis of complex data
Authors: Freeman Tom C. , Horsewell Sebastian , Patir Anirudh , Harling-Lee Josh , Regan Tim , Shih Barbara B. , Prendergast James , Hume David A. , Angus Tim 
Published: September 2020

AbstractQuantitative and qualitative data derived from the analysis of genomes, genes, proteins or metabolites from tissue or cells are currently generated in huge volumes during biomedical research. Graphia is an open-source platform created for the graph-based analysis of such complex data, e.g. transcriptomics, proteomics, genomics data. The software imports data already defined as a network or a similarity matrix and is designed to rapidly visualise very large graphs in 2D or 3D space, providing a wide range of functionality for graph exploration. An extensive range of analysis algorithms, routines for graph transformation, and options for the visualisation of node and edge attributes are also available. Graphia’s core is extensible through the deployment of plugins, supporting rapid development of additional computational analyses and features necessary for a given analysis task or data source. A plugin for correlation network analysis is distributed with the core application, to support the generation of correlation graphs from any tabular matrix of continuous or discrete values. This provides a powerful analysis solution for the interpretation of high-dimensional data from many sources. Several use cases of Graphia are described, to showcase its wide range of applications. Graphia runs on all major desktop operating systems and is freely available to download fromhttps://graphia.app/.
Deleterious impacts of inactivity and beneficial impacts of neuromuscular electrical stimulation on muscle structure and function in the zebrafish model of Duchenne Muscular Dystrophy
Authors: Kilroy Elisabeth A. , Brann Kaylee L. , Schaffer Claire E. , Varney Devon , Silknitter Kodey J. , Miner Jordan N. , Almaghasilah Ahmed , Spellen Tashawna L. , Lewis Alexandra D. , Tilbury Karissa , King Benjamin L. , Kelley Joshua B. , Henry Clarissa A. 
Published: September 2020

AbstractAlthough it is known that inactivity is deleterious for healthy individuals, less is known about the consequences of inactivity on muscle disease. Reduced activity is frequently encouraged for individuals with congenital muscular dystrophies such as Duchenne Muscular Dystrophy (DMD). We used the zebrafishdmdmutant and a longitudinal design to elucidate the consequences of inactivity versus activity on muscle health. Inactivity worsened muscle structure and survival. We designed four neuromuscular stimulation paradigms loosely based on weight lifting regimens. Each paradigm differentially affected muscle structure, function, and survival. Only endurance neuromuscular stimulation (eNMES) improved all outcome measures. We found that eNMES (1) returns gene expression to wild-type levels, (2) increases muscle adhesion to the extracellular matrix (ECM), and (3) remodels the ECM and supports regeneration. Our data indicate that inactivity is deleterious but neuromuscular stimulation can be beneficial, suggesting that the right type of activity may benefit patients with muscle disease.