scholarly journals Sleep Modelling across Physiological Levels

2019 ◽  
Vol 1 (1) ◽  
pp. 166-184 ◽  
Author(s):  
Svetlana Postnova
Keyword(s):  
Systems Biology ◽  
Circadian Rhythms ◽  
Glial Cells ◽  
Large Scale ◽  
Integrated Systems ◽  
Brain Dynamics ◽  
Sleep Regulation ◽  
Underlying Mechanisms ◽  
Different Levels ◽  
Reductionist Approach

Sleep and circadian rhythms are regulated across multiple functional, spatial and temporal levels: from genes to networks of coupled neurons and glial cells, to large scale brain dynamics and behaviour. The dynamics at each of these levels are complex and the interaction between the levels is even more so, so research have mostly focused on interactions within the levels to understand the underlying mechanisms—the so-called reductionist approach. Mathematical models were developed to test theories of sleep regulation and guide new experiments at each of these levels and have become an integral part of the field. The advantage of modelling, however, is that it allows us to simulate and test the dynamics of complex biological systems and thus provides a tool to investigate the connections between the different levels and study the system as a whole. In this paper I review key models of sleep developed at different physiological levels and discuss the potential for an integrated systems biology approach for sleep regulation across these levels. I also highlight the necessity of building mechanistic connections between models of sleep and circadian rhythms across these levels.

scholarly journals LipidLynxX: a data transfer hub to support integration of large scale lipidomics datasets

2020 ◽  
Author(s):  
Zhixu Ni ◽  
Maria Fedorova
Keyword(s):  
Systems Biology ◽  
Data Integration ◽  
High Throughput ◽  
Large Scale ◽  
Data Transfer ◽  
Structural Information ◽  
Meta Analysis ◽  
Health And Disease ◽  
Different Levels ◽  
Cross Match

AbstractModern high throughput lipidomics provides large-scale datasets reporting hundreds of lipid molecular species. However, cross-laboratory comparison, meta-analysis, and systems biology integration of in-house generated and published datasets remain challenging due to a high diversity of used lipid annotation systems, different levels of reported structural information, and shortage in links to data integration resources. To support lipidomics data integration and interoperability of experimental lipidomics with data integration tools, we developed LipidLynxX serving as a hub facilitating data flow from high-throughput lipidomics analysis to systems biology data integration. LipidLynxX provides the possibility to convert, cross-match, and link various lipid annotations to the tools supporting lipid ontology, pathway, and network analysis aiming systems-wide integration and functional annotation of lipidome dynamics in health and disease. LipidLynxX is a flexible, customizable open-access tool freely available for download at https://github.com/SysMedOs/LipidLynxX.

Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

2019 ◽  
Vol 42 ◽  
Author(s):  
J. Alfredo Blakeley-Ruiz ◽  
Carlee S. McClintock ◽  
Ralph Lydic ◽  
Helen A. Baghdoyan ◽  
James J. Choo ◽  
...  
Keyword(s):  
Systems Biology ◽  
High Resolution ◽  
Experimental Design ◽  
Integrated Systems ◽  
Microbiome Research ◽  
Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

Evolution of Metastable Structures in Bimetallic Catalysts from Microscopy and Machine-Learning Molecular Dynamics

2020 ◽  
Author(s):  
Jin Soo Lim ◽  
Jonathan Vandermause ◽  
Matthijs A. van Spronsen ◽  
Albert Musaelian ◽  
Christopher R. O’Connor ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Complete Characterization ◽  
Layer By Layer ◽  
Surface Restructuring ◽  
Metastable Structures ◽  
Mechanistic Investigation ◽  
Underlying Mechanisms

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.

Inflammatory Biomarkers in Atrial Fibrillation

2019 ◽  
Vol 26 (5) ◽  
pp. 837-854 ◽  
Author(s):  
Effimia Zacharia ◽  
Nikolaos Papageorgiou ◽  
Adam Ioannou ◽  
Gerasimos Siasos ◽  
Spyridon Papaioannou ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Plasma Levels ◽  
Large Scale ◽  
Inflammatory Biomarkers ◽  
Inflammatory Pathways ◽  
Inflammatory State ◽  
Anti Inflammatory ◽  
Underlying Mechanisms

During the last few years, a significant number of studies have attempted to clarify the underlying mechanisms that lead to the presentation of atrial fibrillation (AF). Inflammation is a key component of the pathophysiological processes that lead to the development of AF; the amplification of inflammatory pathways triggers AF, and, in tandem, AF increases the inflammatory state. Indeed, the plasma levels of several inflammatory biomarkers are elevated in patients with AF. In addition, the levels of specific inflammatory biomarkers may provide information regarding to the AF duration. Several small studies have assessed the role of anti-inflammatory treatment in atrial fibrillation but the results have been contradictory. Large-scale studies are needed to evaluate the role of inflammation in AF and whether anti-inflammatory medications should be routinely administered to patients with AF.

scholarly journals On the structural connectivity of large-scale models of brain networks at cellular level

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giuseppe Giacopelli ◽  
Domenico Tegolo ◽  
Emiliano Spera ◽  
Michele Migliore
Keyword(s):  
Large Scale ◽  
Brain Networks ◽  
Structural Connectivity ◽  
Network Models ◽  
Brain Regions ◽  
Cellular Level ◽  
Scale Model ◽  
Mathematical Framework ◽  
Underlying Mechanisms ◽  
Experimental Findings

AbstractThe brain’s structural connectivity plays a fundamental role in determining how neuron networks generate, process, and transfer information within and between brain regions. The underlying mechanisms are extremely difficult to study experimentally and, in many cases, large-scale model networks are of great help. However, the implementation of these models relies on experimental findings that are often sparse and limited. Their predicting power ultimately depends on how closely a model’s connectivity represents the real system. Here we argue that the data-driven probabilistic rules, widely used to build neuronal network models, may not be appropriate to represent the dynamics of the corresponding biological system. To solve this problem, we propose to use a new mathematical framework able to use sparse and limited experimental data to quantitatively reproduce the structural connectivity of biological brain networks at cellular level.

scholarly journals Potential Energy Implications of Connected and Automated Vehicles: Exploring Key Leverage Points through Scenario Screening and Analysis

2019 ◽  
Vol 2673 (5) ◽  
pp. 84-94 ◽  
Author(s):  
Brian Bush ◽  
Laura Vimmerstedt ◽  
Jeff Gonder
Keyword(s):  
Systems Engineering ◽  
Large Scale ◽  
Operating Cost ◽  
Dynamics Model ◽  
Transportation Service ◽  
Service Outcomes ◽  
Behavioral Parameters ◽  
Computationally Intensive ◽  
Different Levels ◽  
Selection Of

Connected and automated vehicle (CAV) technologies could transform the transportation system over the coming decades, but face vehicle and systems engineering challenges, as well as technological, economic, demographic, and regulatory issues. The authors have developed a system dynamics model for generating, analyzing, and screening self-consistent CAV adoption scenarios. Results can support selection of scenarios for subsequent computationally intensive study using higher-resolution models. The potential for and barriers to large-scale adoption of CAVs have been analyzed using preliminary quantitative data and qualitative understandings of system relationships among stakeholders across the breadth of these issues. Although they are based on preliminary data, the results map possibilities for achieving different levels of CAV adoption and system-wide fuel use and demonstrate the interplay of behavioral parameters such as how consumers value their time versus financial parameters such as operating cost. By identifying the range of possibilities, estimating the associated energy and transportation service outcomes, and facilitating screening of scenarios for more detailed analysis, this work could inform transportation planners, researchers, and regulators.

Educating Democratic Character

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Natalia Rogach Alexander ◽  
Philip Kitcher
Keyword(s):  
Large Scale ◽  
Democratic Education ◽  
Political Life ◽  
Individual Experience ◽  
Main Work ◽  
Mutual Engagement ◽  
Democratic Character ◽  
Imminent Death ◽  
Different Levels

Abstract Many recent writers on democracy have lamented its decay and warned of its imminent death. We argue that the concerns are focused at three different levels of democracy. The most fundamental of these, celebrated by Tocqueville and by Dewey, recognizes the interactions and joint deliberations among citizens who seek sympathetic mutual engagement. Such engagement is increasingly rare in large-scale political life. In diagnosing and treating the problems, we recommend returning to the debate between Lippmann and Dewey, in which many of the concerns now prominent were already voiced. This inspires the main work of the paper – the reconstruction of Dewey’s conception of democracy as a ‘mode of associated living’. We focus on the thesis that democracy is educative and explicate Dewey’s notion of growth, showing how democratic education contributes to three important functions: the capacity for sustaining oneself, the enrichment of individual experience, and the ability to enter into cooperative discussions with fellow citizens. Dewey’s conception of democratic education is directed at fostering particular virtues and, if citizens come to possess them, the need for Lippmann’s ‘omnicompetent individual’ vanishes. We conclude by suggesting that Dewey’s project of educating democratic character is pertinent for addressing the disaffection of our times.

Construction of Essential Care Service Package for People Living with Dementia in Smoke-free Environment under Disease Pandemic in China

2021 ◽  
Vol 7 (4) ◽  
pp. 308-325
Author(s):  
Tongda Sun ◽  
Hongdao Meng ◽  
Mingze Zhu ◽  
Xiaoxin Dong ◽  
Naidan Tu ◽  
...  
Keyword(s):  
Large Scale ◽  
Care Service ◽  
Cluster Sampling ◽  
Service Needs ◽  
Public Attention ◽  
Term Care ◽  
Service Package ◽  
Care Services ◽  
Free Environment ◽  
Different Levels

Objectives: In recent years, the harm of smoking has attracted more and more public attention. Creating a healthy smoke-free environment has been widely favored and supported by the public. Smokeless environment has a certain positive effect on the rehabilitation of dementia patients. Sustained smoking cessation is associated with significantly decreased the future prevalence of dementia. Therefore, hospitals often establish a special organizational structure and management model for tobacco control, and carry out training and assessment for all staff. The nursing group also took it as the basic nursing standard. The 2019 disease pandemic has posed unique health threats to people living with dementia (PLWD). Therefore, a strict smoke-free environment is more necessary for the nursing group. One of the key challenges is scaling up long-term care services to meet the needs of the rapidly growing population of PLWD in developing countries. The aim of the study is to explore the care service needs, utilization and build an essential care service package (ECSP) for PLWD under the disease pandemic in China. Methods: From July 2018 to October 2019, a total of 1255 elderly with dementia in six cities in China by a cluster sampling were investigated with the self-designed questionnaire. Care service needs and utilization for PLWD with different levels of cognitive impairment were summarized. Results: The ECSP for PLWD was composed of 30 service items (7 for core care) in order to guarantee that all PLWD enjoy equal care services, basing on public financing and implementing strategies and taking China's situations into account. The selection plan for ECSP at different levels is designed as 'General Care Services + Selective Care Services ', in which respective service items for low, mid, and high-level care for PLWD are 7+3, 7+6, and 7+10, and requires 151.41 hours, 201.88 hours, and 252.35 hours per month, respectively. Conclusion: The present study provides the first large-scale data on care service needs and utilization for PLWD in mainland China. The ECSP for PLWD based on the needs advanced in the paper was a practicable and effective quantitative management means that deserves a large-scale application. Some safeguard mechanisms and operational implementing pathways of ECSP for PLWD during and after the disease pandemic in China are proposed.

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