scholarly journals Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology

2015 ◽  
Author(s):  
Marco Fondi ◽  
Pietro Liò
Keyword(s):  
Systems Biology ◽  
Large Scale ◽  
Biological Information ◽  
Special Focus ◽  
Metabolic Modelling ◽  
Microbial Life ◽  
Multi Scale ◽  
Integrated Omics ◽  
Molecular Components ◽  
Omics Data Integration

Integrated -omics approaches are quickly spreading across microbiology research labs, leading to i) the possibility of detecting previously hidden features of microbial cells like multi-scale spatial organisation and ii) tracing molecular components across multiple cellular functional states. This promises to reduce the knowledge gap between genotype and phenotype and poses new challenges for computational microbiologists. We underline how the capability to unravel the complexity of microbial life will strongly depend on the integration of the huge and diverse amount of information that can be derived today from -omics experiments. In this work, we present opportunities and challenges of multi –omics data integration in current systems biology pipelines. We here discuss which layers of biological information are important for biotechnological and clinical purposes, with a special focus on bacterial metabolism and modelling procedures. A general review of the most recent computational tools for performing large-scale datasets integration is also presented, together with a possible framework to guide the design of systems biology experiments by microbiologists.

scholarly journals Public Awareness: What Climate Change Scientists Should Consider

2020 ◽  
Vol 12 (20) ◽  
pp. 8369
Author(s):  
Mohammad Rahimi
Keyword(s):  
Climate Change ◽  
Social Media ◽  
Large Scale ◽  
Public Awareness ◽  
Connected Network ◽  
Multi Scale ◽  
Valuable Addition ◽  
Scientific Approach ◽  
Design Solutions ◽  
Mitigate Climate Change

In this Opinion, the importance of public awareness to design solutions to mitigate climate change issues is highlighted. A large-scale acknowledgment of the climate change consequences has great potential to build social momentum. Momentum, in turn, builds motivation and demand, which can be leveraged to develop a multi-scale strategy to tackle the issue. The pursuit of public awareness is a valuable addition to the scientific approach to addressing climate change issues. The Opinion is concluded by providing strategies on how to effectively raise public awareness on climate change-related topics through an integrated, well-connected network of mavens (e.g., scientists) and connectors (e.g., social media influencers).

scholarly journals Multi-Scale Ionospheric Anomalies Monitoring and Spatio-Temporal Analysis during Intense Storm

Atmosphere ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 215
Author(s):  
Na Cheng ◽  
Shuli Song ◽  
Wei Li
Keyword(s):  
Magnetic Storm ◽  
Large Scale ◽  
Temporal Dynamics ◽  
Ionospheric Disturbance ◽  
Ionospheric Scintillation ◽  
Small Scale ◽  
Electron Content ◽  
Total Electron ◽  
Multi Scale ◽  
Intense Storm

The ionosphere is a significant component of the geospace environment. Storm-induced ionospheric anomalies severely affect the performance of Global Navigation Satellite System (GNSS) Positioning, Navigation, and Timing (PNT) and human space activities, e.g., the Earth observation, deep space exploration, and space weather monitoring and prediction. In this study, we present and discuss the multi-scale ionospheric anomalies monitoring over China using the GNSS observations from the Crustal Movement Observation Network of China (CMONOC) during the 2015 St. Patrick’s Day storm. Total Electron Content (TEC), Ionospheric Electron Density (IED), and the ionospheric disturbance index are used to monitor the storm-induced ionospheric anomalies. This study finally reveals the occurrence of the large-scale ionospheric storms and small-scale ionospheric scintillation during the storm. The results show that this magnetic storm was accompanied by a positive phase and a negative phase ionospheric storm. At the beginning of the main phase of the magnetic storm, both TEC and IED were significantly enhanced. There was long-duration depletion in the topside ionospheric TEC during the recovery phase of the storm. This study also reveals the response and variations in regional ionosphere scintillation. The Rate of the TEC Index (ROTI) was exploited to investigate the ionospheric scintillation and compared with the temporal dynamics of vertical TEC. The analysis of the ROTI proved these storm-induced TEC depletions, which suppressed the occurrence of the ionospheric scintillation. To improve the spatial resolution for ionospheric anomalies monitoring, the regional Three-Dimensional (3D) ionospheric model is reconstructed by the Computerized Ionospheric Tomography (CIT) technique. The spatial-temporal dynamics of ionospheric anomalies during the severe geomagnetic storm was reflected in detail. The IED varied with latitude and altitude dramatically; the maximum IED decreased, and the area where IEDs were maximum moved southward.

scholarly journals MuSA: a graphical user interface for multi-OMICs data integration in radiogenomic studies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mario Zanfardino ◽  
Rossana Castaldo ◽  
Katia Pane ◽  
Ornella Affinito ◽  
Marco Aiello ◽  
...  
Keyword(s):  
User Interface ◽  
Data Integration ◽  
Graphical User Interface ◽  
Data Science ◽  
Heterogeneous Data ◽  
Biological Information ◽  
Omics Data ◽  
Correlation Clustering ◽  
Downstream Analysis ◽  
Omics Data Integration

AbstractAnalysis of large-scale omics data along with biomedical images has gaining a huge interest in predicting phenotypic conditions towards personalized medicine. Multiple layers of investigations such as genomics, transcriptomics and proteomics, have led to high dimensionality and heterogeneity of data. Multi-omics data integration can provide meaningful contribution to early diagnosis and an accurate estimate of prognosis and treatment in cancer. Some multi-layer data structures have been developed to integrate multi-omics biological information, but none of these has been developed and evaluated to include radiomic data. We proposed to use MultiAssayExperiment (MAE) as an integrated data structure to combine multi-omics data facilitating the exploration of heterogeneous data. We improved the usability of the MAE, developing a Multi-omics Statistical Approaches (MuSA) tool that uses a Shiny graphical user interface, able to simplify the management and the analysis of radiogenomic datasets. The capabilities of MuSA were shown using public breast cancer datasets from TCGA-TCIA databases. MuSA architecture is modular and can be divided in Pre-processing and Downstream analysis. The pre-processing section allows data filtering and normalization. The downstream analysis section contains modules for data science such as correlation, clustering (i.e., heatmap) and feature selection methods. The results are dynamically shown in MuSA. MuSA tool provides an easy-to-use way to create, manage and analyze radiogenomic data. The application is specifically designed to guide no-programmer researchers through different computational steps. Integration analysis is implemented in a modular structure, making MuSA an easily expansible open-source software.

scholarly journals Multi-scale modelling of a large scale shell-and-tube latent heat storage system for direct steam generation power plants

2020 ◽  
Author(s):  
Clément Beust ◽  
Erwin Franquet ◽  
Jean-Pierre Bédécarrats ◽  
Pierre Garcia ◽  
Jérôme Pouvreau ◽  
...  
Keyword(s):  
Power Plants ◽  
Large Scale ◽  
Storage System ◽  
Steam Generation ◽  
Latent Heat Storage ◽  
Multi Scale ◽  
Direct Steam ◽  
Scale Modelling ◽  
Shell And Tube ◽  
Generation Power

Integrating landscape resistance and multi-scale predictor of habitat selection for amphibian distribution modelling at large scale

2021 ◽  
Author(s):  
Florence Matutini ◽  
Jacques Baudry ◽  
Marie-Josée Fortin ◽  
Guillaume Pain ◽  
Joséphine Pithon
Keyword(s):  
Habitat Selection ◽  
Large Scale ◽  
Landscape Resistance ◽  
Distribution Modelling ◽  
Multi Scale ◽  
Selection For

scholarly journals Hybrid Graph Neural Networks for Crowd Counting

2020 ◽  
Vol 34 (07) ◽  
pp. 11693-11700 ◽  
Author(s):  
Ao Luo ◽  
Fan Yang ◽  
Xin Li ◽  
Dong Nie ◽  
Zhicheng Jiao ◽  
...  
Keyword(s):  
Network Architecture ◽  
Message Passing ◽  
Large Scale ◽  
State Of The Art ◽  
Density Variation ◽  
Feature Maps ◽  
Crowd Counting ◽  
Multi Scale ◽  
Crowd Density ◽  
Graph Neural Networks

Crowd counting is an important yet challenging task due to the large scale and density variation. Recent investigations have shown that distilling rich relations among multi-scale features and exploiting useful information from the auxiliary task, i.e., localization, are vital for this task. Nevertheless, how to comprehensively leverage these relations within a unified network architecture is still a challenging problem. In this paper, we present a novel network structure called Hybrid Graph Neural Network (HyGnn) which targets to relieve the problem by interweaving the multi-scale features for crowd density as well as its auxiliary task (localization) together and performing joint reasoning over a graph. Specifically, HyGnn integrates a hybrid graph to jointly represent the task-specific feature maps of different scales as nodes, and two types of relations as edges: (i) multi-scale relations capturing the feature dependencies across scales and (ii) mutual beneficial relations building bridges for the cooperation between counting and localization. Thus, through message passing, HyGnn can capture and distill richer relations between nodes to obtain more powerful representations, providing robust and accurate results. Our HyGnn performs significantly well on four challenging datasets: ShanghaiTech Part A, ShanghaiTech Part B, UCF_CC_50 and UCF_QNRF, outperforming the state-of-the-art algorithms by a large margin.

scholarly journals Functionalized Carbon Nanotubes (CNTs) for Water and Wastewater Treatment: Preparation to Application

2021 ◽  
Vol 13 (10) ◽  
pp. 5717
Author(s):  
Mian Muhammad-Ahson Aslam ◽  
Hsion-Wen Kuo ◽  
Walter Den ◽  
Muhammad Usman ◽  
Muhammad Sultan ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Wastewater Treatment ◽  
Water Resources ◽  
Large Scale ◽  
Industrial Applications ◽  
Biological Species ◽  
Special Focus ◽  
Water And Wastewater Treatment ◽  
Adsorption Sites ◽  
Water And Wastewater

As the world human population and industrialization keep growing, the water availability issue has forced scientists, engineers, and legislators of water supply industries to better manage water resources. Pollutant removals from wastewaters are crucial to ensure qualities of available water resources (including natural water bodies or reclaimed waters). Diverse techniques have been developed to deal with water quality concerns. Carbon based nanomaterials, especially carbon nanotubes (CNTs) with their high specific surface area and associated adsorption sites, have drawn a special focus in environmental applications, especially water and wastewater treatment. This critical review summarizes recent developments and adsorption behaviors of CNTs used to remove organics or heavy metal ions from contaminated waters via adsorption and inactivation of biological species associated with CNTs. Foci include CNTs synthesis, purification, and surface modifications or functionalization, followed by their characterization methods and the effect of water chemistry on adsorption capacities and removal mechanisms. Functionalized CNTs have been proven to be promising nanomaterials for the decontamination of waters due to their high adsorption capacity. However, most of the functional CNT applications are limited to lab-scale experiments only. Feasibility of their large-scale/industrial applications with cost-effective ways of synthesis and assessments of their toxicity with better simulating adsorption mechanisms still need to be studied.

Simultaneous Segmentation of Fetal Hearts and Lungs for Medical Ultrasound Images via an Efficient Multi-scale Model Integrated With Attention Mechanism

2021 ◽  
pp. 016173462110425
Author(s):  
Jianing Xi ◽  
Jiangang Chen ◽  
Zhao Wang ◽  
Dean Ta ◽  
Bing Lu ◽  
...  
Keyword(s):  
Congenital Anomaly ◽  
Large Scale ◽  
Automatic Segmentation ◽  
Receptive Fields ◽  
Semantic Segmentation ◽  
Attention Mechanism ◽  
Scale Model ◽  
Ultrasound Images ◽  
Multi Scale ◽  
Task Irrelevant

Large scale early scanning of fetuses via ultrasound imaging is widely used to alleviate the morbidity or mortality caused by congenital anomalies in fetal hearts and lungs. To reduce the intensive cost during manual recognition of organ regions, many automatic segmentation methods have been proposed. However, the existing methods still encounter multi-scale problem at a larger range of receptive fields of organs in images, resolution problem of segmentation mask, and interference problem of task-irrelevant features, obscuring the attainment of accurate segmentations. To achieve semantic segmentation with functions of (1) extracting multi-scale features from images, (2) compensating information of high resolution, and (3) eliminating the task-irrelevant features, we propose a multi-scale model with skip connection framework and attention mechanism integrated. The multi-scale feature extraction modules are incorporated with additive attention gate units for irrelevant feature elimination, through a U-Net framework with skip connections for information compensation. The performance of fetal heart and lung segmentation indicates the superiority of our method over the existing deep learning based approaches. Our method also shows competitive performance stability during the task of semantic segmentations, showing a promising contribution on ultrasound based prognosis of congenital anomaly in the early intervention, and alleviating the negative effects caused by congenital anomaly.

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