Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

2011 ◽  
Vol 80 (1) ◽  
pp. 273-299 ◽  
Author(s):  
Jürgen Cox ◽  
Matthias Mann
2019 ◽  
Vol 218 ◽  
pp. 481-504 ◽  
Author(s):  
Caroline Gauchotte-Lindsay ◽  
Thomas J. Aspray ◽  
Mara Knapp ◽  
Umer Z. Ijaz

We present here a data-driven systems biology framework for the rational design of biotechnological solutions for contaminated environments with the aim of understanding the interactions and mechanisms underpinning the role of microbial communities in the biodegradation of contaminated soils.


2019 ◽  
Vol 42 ◽  
Author(s):  
J. Alfredo Blakeley-Ruiz ◽  
Carlee S. McClintock ◽  
Ralph Lydic ◽  
Helen A. Baghdoyan ◽  
James J. Choo ◽  
...  

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.


Machines ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 13
Author(s):  
Yuhang Yang ◽  
Zhiqiao Dong ◽  
Yuquan Meng ◽  
Chenhui Shao

High-fidelity characterization and effective monitoring of spatial and spatiotemporal processes are crucial for high-performance quality control of many manufacturing processes and systems in the era of smart manufacturing. Although the recent development in measurement technologies has made it possible to acquire high-resolution three-dimensional (3D) surface measurement data, it is generally expensive and time-consuming to use such technologies in real-world production settings. Data-driven approaches that stem from statistics and machine learning can potentially enable intelligent, cost-effective surface measurement and thus allow manufacturers to use high-resolution surface data for better decision-making without introducing substantial production cost induced by data acquisition. Among these methods, spatial and spatiotemporal interpolation techniques can draw inferences about unmeasured locations on a surface using the measurement of other locations, thus decreasing the measurement cost and time. However, interpolation methods are very sensitive to the availability of measurement data, and their performances largely depend on the measurement scheme or the sampling design, i.e., how to allocate measurement efforts. As such, sampling design is considered to be another important field that enables intelligent surface measurement. This paper reviews and summarizes the state-of-the-art research in interpolation and sampling design for surface measurement in varied manufacturing applications. Research gaps and future research directions are also identified and can serve as a fundamental guideline to industrial practitioners and researchers for future studies in these areas.


Sensors ◽  
2021 ◽  
Vol 21 (2) ◽  
pp. 464
Author(s):  
Wei Ma ◽  
Sean Qian

Recent decades have witnessed the breakthrough of autonomous vehicles (AVs), and the sensing capabilities of AVs have been dramatically improved. Various sensors installed on AVs will be collecting massive data and perceiving the surrounding traffic continuously. In fact, a fleet of AVs can serve as floating (or probe) sensors, which can be utilized to infer traffic information while cruising around the roadway networks. Unlike conventional traffic sensing methods relying on fixed location sensors or moving sensors that acquire only the information of their carrying vehicle, this paper leverages data from AVs carrying sensors for not only the information of the AVs, but also the characteristics of the surrounding traffic. A high-resolution data-driven traffic sensing framework is proposed, which estimates the fundamental traffic state characteristics, namely, flow, density and speed in high spatio-temporal resolutions and of each lane on a general road, and it is developed under different levels of AV perception capabilities and for any AV market penetration rate. Experimental results show that the proposed method achieves high accuracy even with a low AV market penetration rate. This study would help policymakers and private sectors (e.g., Waymo) to understand the values of massive data collected by AVs in traffic operation and management.


2021 ◽  
Vol 13 (12) ◽  
pp. 2326
Author(s):  
Xiaoyong Li ◽  
Xueru Bai ◽  
Feng Zhou

A deep-learning architecture, dubbed as the 2D-ADMM-Net (2D-ADN), is proposed in this article. It provides effective high-resolution 2D inverse synthetic aperture radar (ISAR) imaging under scenarios of low SNRs and incomplete data, by combining model-based sparse reconstruction and data-driven deep learning. Firstly, mapping from ISAR images to their corresponding echoes in the wavenumber domain is derived. Then, a 2D alternating direction method of multipliers (ADMM) is unrolled and generalized to a deep network, where all adjustable parameters in the reconstruction layers, nonlinear transform layers, and multiplier update layers are learned by an end-to-end training through back-propagation. Since the optimal parameters of each layer are learned separately, 2D-ADN exhibits more representation flexibility and preferable reconstruction performance than model-driven methods. Simultaneously, it is able to better facilitate ISAR imaging with limited training samples than data-driven methods owing to its simple structure and small number of adjustable parameters. Additionally, benefiting from the good performance of 2D-ADN, a random phase error estimation method is proposed, through which well-focused imaging can be acquired. It is demonstrated by experiments that although trained by only a few simulated images, the 2D-ADN shows good adaptability to measured data and favorable imaging results with a clear background can be obtained in a short time.


2021 ◽  
Vol 303 ◽  
pp. 117656
Author(s):  
Maitreyee Dey ◽  
Soumya Prakash Rana ◽  
Clarke V. Simmons ◽  
Sandra Dudley

Author(s):  
Jose N. Paredes ◽  
Gerardo I. Simari ◽  
Maria Vanina Martinez ◽  
Marcelo A. Falappa

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