Spatial heterogeneity of the cytosol revealed by machine learning-based 3D particle tracking

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McLaughlin, G. A., Langdon, E. M., Crutchley, J. M., Holt, L. J., Forest, M. G., Newby, J. M., & Gladfelter, A. S. (2020). Spatial heterogeneity of the cytosol revealed by machine learning-based 3D particle tracking. Molecular Biology of the Cell, 31(14), 1498-1511, doi:10.1091/mbc.E20-03-0210.The spatial structure and physical properties of the cytosol are not well understood. Measurements of the material state of the cytosol are challenging due to its spatial and temporal heterogeneity. Recent development of genetically encoded multimeric nanoparticles (GEMs) has opened up study of the cytosol at the length scales of multiprotein complexes (20-60 nm). We developed an image analysis pipeline for 3D imaging of GEMs in the context of large, multinucleate fungi where there is evidence of functional compartmentalization of the cytosol for both the nuclear division cycle and branching. We applied a neural network to track particles in 3D and then created quantitative visualizations of spatially varying diffusivity. Using this pipeline to analyze spatial diffusivity patterns, we found that there is substantial variability in the properties of the cytosol. We detected zones where GEMs display especially low diffusivity at hyphal tips and near some nuclei, showing that the physical state of the cytosol varies spatially within a single cell. Additionally, we observed significant cell-to-cell variability in the average diffusivity of GEMs. Thus, the physical properties of the cytosol vary substantially in time and space and can be a source of heterogeneity within individual cells and across populations.We would like to thank the 2016 Physiology course and Christina Termini at the Marine Biological Laboratory in Woods Hole, MA, Gregory Brittingham, and Marcus Roper for initial experiments and perspectives on pipeline. We thank David Adalsteinsson for help with DataTank software and many conversations about image analysis on large datasets. We thank Emmanual Levy (Weizmann Institute) for providing plasmids encoding synthetic phase separating peptides. This work was supported by Google Cloud, the National Science Foundation (NSF), the National Institutes of Health (NIH), and the Natural Sciences and Engineering Research Council of Canada (NSERC). ASG, EML, and GAM were supported by the NSF (RoLs: 1840273), HHMI faculty scholar award and the NIH (R01GM081506). JMN was supported by the NSERC (RGPIN-2019-06435, RGPAS-2019-00014, DGECR-2019-00321) and the NSF (DMS-171474). MGF was supported by the NSF (DMS-1816630, DMS-1664645). LJH was supported by the NIH (R01GM132447)

Physics-Informed Computer Vision: A Review and Perspectives

Incorporation of physical information in machine learning frameworks are opening and transforming many application domains. Here the learning process is augmented through the induction of fundamental knowledge and governing physical laws. In this work we explore their utility for computer vision tasks in interpreting and understanding visual data. We present a systematic literature review of formulation and approaches to computer vision tasks guided by physical laws. We begin by decomposing the popular computer vision pipeline into a taxonomy of stages and investigate approaches to incorporate governing physical equations in each stage. Existing approaches in each task are analyzed with regard to what governing physical processes are modeled, formulated and how they are incorporated, i.e. modify data (observation bias), modify networks (inductive bias), and modify losses (learning bias). The taxonomy offers a unified view of the application of the physics-informed capability, highlighting where physics-informed learning has been conducted and where the gaps and opportunities are. Finally, we highlight open problems and challenges to inform future research. While still in its early days, the study of physics-informed computer vision has the promise to develop better computer vision models that can improve physical plausibility, accuracy, data efficiency and generalization in increasingly realistic applications

Visual analytics of location-based social networks for decision support

Recent advances in technology have enabled people to add location information to social networks called Location-Based Social Networks (LBSNs) where people share their communication and whereabouts not only in their daily lives, but also during abnormal situations, such as crisis events. However, since the volume of the data exceeds the boundaries of human analytical capabilities, it is almost impossible to perform a straightforward qualitative analysis of the data. The emerging field of visual analytics has been introduced to tackle such challenges by integrating the approaches from statistical data analysis and human computer interaction into highly interactive visual environments. Based on the idea of visual analytics, this research contributes the techniques of knowledge discovery in social media data for providing comprehensive situational awareness. We extract valuable hidden information from the huge volume of unstructured social media data and model the extracted information for visualizing meaningful information along with user-centered interactive interfaces. We develop visual analytics techniques and systems for spatial decision support through coupling modeling of spatiotemporal social media data, with scalable and interactive visual environments. These systems allow analysts to detect and examine abnormal events within social media data by integrating automated analytical techniques and visual methods. We provide comprehensive analysis of public behavior response in disaster events through exploring and examining the spatial and temporal distribution of LBSNs. We also propose a trajectory-based visual analytics of LBSNs for anomalous human movement analysis during crises by incorporating a novel classification technique. Finally, we introduce a visual analytics approach for forecasting the overall flow of human crowds

Anomalous transport in the crowded world of biological cells

A ubiquitous observation in cell biology is that diffusion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarising their densely packed and heterogeneous structures. The most familiar phenomenon is a power-law increase of the MSD, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations, non-gaussian distributions of the displacements, heterogeneous diffusion, and immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarise some widely used theoretical models: gaussian models like FBM and Langevin equations for visco-elastic media, the CTRW model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Emphasis is put on the spatio-temporal properties of the transport in terms of 2-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even for identical MSDs. Then, we review the theory underlying common experimental techniques in the presence of anomalous transport: single-particle tracking, FCS, and FRAP. We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where model systems mimic physiological crowding conditions. Finally, computer simulations play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.Comment: review article, to appear in Rep. Prog. Phy

Hyperbolic Balance Laws: modeling, analysis, and numerics (hybrid meeting)

This workshop brought together leading experts, as well as the most promising young researchers, working on nonlinear hyperbolic balance laws. The meeting focused on addressing new cutting-edge research in modeling, analysis, and numerics. Particular topics included ill-/well-posedness, randomness and multiscale modeling, flows in a moving domain, free boundary problems, games and control

Understanding citizen science and environmental monitoring: final report on behalf of UK Environmental Observation Framework

Citizen science can broadly be defined as the involvement of volunteers in science. Over the past decade there has been a rapid increase in the number of citizen science initiatives. The breadth of environmental-based citizen science is immense. Citizen scientists have surveyed for and monitored a broad range of taxa, and also contributed data on weather and habitats reflecting an increase in engagement with a diverse range of observational science. Citizen science has taken many varied approaches from citizen-led (co-created) projects with local community groups to, more commonly, scientist-led mass participation initiatives that are open to all sectors of society. Citizen science provides an indispensable means of combining environmental research with environmental education and wildlife recording. Here we provide a synthesis of extant citizen science projects using a novel cross-cutting approach to objectively assess understanding of citizen science and environmental monitoring including: 1. Brief overview of knowledge on the motivations of volunteers. 2. Semi-systematic review of environmental citizen science projects in order to understand the variety of extant citizen science projects. 3. Collation of detailed case studies on a selection of projects to complement the semi-systematic review. 4. Structured interviews with users of citizen science and environmental monitoring data focussing on policy, in order to more fully understand how citizen science can fit into policy needs. 5. Review of technology in citizen science and an exploration of future opportunities

Use of Low-Cost Ambient Particulate Sensors in Nablus, Palestine with Application to the Assessment of Regional Dust Storms

Few air pollutant studies within the Palestinian territories have been reported in the literature. In March–April and May–June of 2018, three low-cost, locally calibrated particulate monitors (AirU’s) were deployed at different elevations and source areas throughout the city of Nablus in Northern West Bank, Palestine. During each of the three-week periods, high but site-to-site similar particulate matter less than 2.5 µm in aerodynamic diameter (PM2.5) and less than 10 µm (PM10) concentrations were observed. The PM2.5 concentrations at the three sampling locations and during both sampling periods averaged 38.2 ± 3.6 µg/m3, well above the World Health Organization’s (WHO) 24 h guidelines. Likewise, the PM10 concentrations exceeded or were just below the WHO’s 24 h guidelines, averaging 48.5 ± 4.3 µg/m3. During both periods, short episodes were identified in which the particulate levels at all three sites increased substantially (≈2×) above the regional baseline. Air mass back trajectory analyses using U.S. National Oceanic and Atmospheric Administration’s (NOAA) Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model suggested that, during these peak episodes, the arriving air masses spent recent days over desert areas (e.g., the Saharan Desert in North Africa). On days with regionally low PM2.5 concentrations (≈20 µg/m3), back trajectory analysis showed that air masses were directed in from the Mediterranean Sea area. Further, the lower elevation (downtown) site often recorded markedly higher particulate levels than the valley wall sites. This would suggest locally derived particulate sources are significant and may be beneficial in the identification of potential remediation options

Building Blocks for IoT Analytics Internet-of-Things Analytics

Internet-of-Things (IoT) Analytics are an integral element of most IoT applications, as it provides the means to extract knowledge, drive actuation services and optimize decision making. IoT analytics will be a major contributor to IoT business value in the coming years, as it will enable organizations to process and fully leverage large amounts of IoT data, which are nowadays largely underutilized. The Building Blocks of IoT Analytics is devoted to the presentation the main technology building blocks that comprise advanced IoT analytics systems. It introduces IoT analytics as a special case of BigData analytics and accordingly presents leading edge technologies that can be deployed in order to successfully confront the main challenges of IoT analytics applications. Special emphasis is paid in the presentation of technologies for IoT streaming and semantic interoperability across diverse IoT streams. Furthermore, the role of cloud computing and BigData technologies in IoT analytics are presented, along with practical tools for implementing, deploying and operating non-trivial IoT applications. Along with the main building blocks of IoT analytics systems and applications, the book presents a series of practical applications, which illustrate the use of these technologies in the scope of pragmatic applications. Technical topics discussed in the book include: Cloud Computing and BigData for IoT analyticsSearching the Internet of ThingsDevelopment Tools for IoT Analytics ApplicationsIoT Analytics-as-a-ServiceSemantic Modelling and Reasoning for IoT AnalyticsIoT analytics for Smart BuildingsIoT analytics for Smart CitiesOperationalization of IoT analyticsEthical aspects of IoT analyticsThis book contains both research oriented and applied articles on IoT analytics, including several articles reflecting work undertaken in the scope of recent European Commission funded projects in the scope of the FP7 and H2020 programmes. These articles present results of these projects on IoT analytics platforms and applications. Even though several articles have been contributed by different authors, they are structured in a well thought order that facilitates the reader either to follow the evolution of the book or to focus on specific topics depending on his/her background and interest in IoT and IoT analytics technologies. The compilation of these articles in this edited volume has been largely motivated by the close collaboration of the co-authors in the scope of working groups and IoT events organized by the Internet-of-Things Research Cluster (IERC), which is currently a part of EU's Alliance for Internet of Things Innovation (AIOTI)

A computer vision system for detecting and analysing critical events in cities

Whether for commuting or leisure, cycling is a growing transport mode in many cities worldwide. However, it is still perceived as a dangerous activity. Although serious incidents related to cycling leading to major injuries are rare, the fear of getting hit or falling hinders the expansion of cycling as a major transport mode. Indeed, it has been shown that focusing on serious injuries only touches the tip of the iceberg. Near miss data can provide much more information about potential problems and how to avoid risky situations that may lead to serious incidents. Unfortunately, there is a gap in the knowledge in identifying and analysing near misses. This hinders drawing statistically significant conclusions to provide measures for the built-environment that ensure a safer environment for people on bikes. In this research, we develop a method to detect and analyse near misses and their risk factors using artificial intelligence. This is accomplished by analysing video streams linked to near miss incidents within a novel framework relying on deep learning and computer vision. This framework automatically detects near misses and extracts their risk factors from video streams before analysing their statistical significance. It also provides practical solutions implemented in a camera with embedded AI (URBAN-i Box) and a cloud-based service (URBAN-i Cloud) to tackle the stated issue in the real-world settings for use by researchers, policy-makers, or citizens. The research aims to provide human-centred evidence that may enable policy-makers and planners to provide a safer built environment for cycling in London, or elsewhere. More broadly, this research aims to contribute to the scientific literature with the theoretical and empirical foundations of a computer vision system that can be utilised for detecting and analysing other critical events in a complex environment. Such a system can be applied to a wide range of events, such as traffic incidents, crime or overcrowding

Living analytics methods for the social web

[no abstract