| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
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| 3. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- Blanco, Jose Luis, et al.
(författare)
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A Kalman Filter Based Approach To Probabilistic Gas Distribution Mapping
- 2013
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Konferensbidrag (refereegranskat)abstract
- Building a model of gas concentrations has important indus-trial and environmental applications, and mobile robots ontheir own or in cooperation with stationary sensors play animportant role in this task. Since an exact analytical de-scription of turbulent flow remains an intractable problem,we propose an approximate approach which not only esti-mates the concentrations but also their variances for eachlocation. Our point of view is that of sequential Bayesianestimation given a lattice of 2D cells treated as hidden vari-ables. We first discuss how a simple Kalman filter pro-vides a solution to the estimation problem. To overcomethe quadratic computational complexity with the mappedarea exhibited by a straighforward application of Kalmanfiltering, we introduce a sparse implementation which runsin constant time. Experimental results for a real robot vali-date the proposed method.
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| 5. |
- Gonzàlez Monroy, Javier, et al.
(författare)
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Probabilistic gas quantification with MOX sensors in open sampling systems : a gaussian process approach
- 2013
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Ingår i: Sensors and actuators. B, Chemical. - : Elsevier. - 0925-4005 .- 1873-3077. ; 188, s. 298-312
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Tidskriftsartikel (refereegranskat)abstract
- Gas quantification based on the response of an array of metal oxide (MOX) gas sensors in an Open Sampling System is a complex problem due to the highly dynamic characteristic of turbulent airflow and the slow dynamics of the MOX sensors. However, many gas related applications require to determine the gas concentration the sensors are being exposed to. Due to the chaotic nature that dominates gas dispersal, in most cases it is desirable to provide, together with an estimate of the mean concentration, an estimate of the uncertainty of the prediction. This work presents a probabilistic approach for gas quantification with an array of MOX gas sensors based on Gaussian Processes, estimating for every measurement of the sensors a posterior distribution of the concentration, from which confidence intervals can be obtained. The proposed approach has been tested with an experimental setup where an array of MOX sensors and a Photo Ionization Detector (PID), used to obtain ground truth concentration, are placed downwind with respect to the gas source. Our approach has been implemented and compared with standard gas quantification methods, demonstrating the advantages when estimating gas concentrations.
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| 6. |
- Luperto, Matteo, et al.
(författare)
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Seeking at-home long-term autonomy of assistive mobile robots through the integration with an IoT-based monitoring system
- 2023
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Ingår i: Robotics and Autonomous Systems. - : Elsevier. - 0921-8890 .- 1872-793X. ; 161
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we propose a system that stems from the integration of an autonomous mobile robot with an IoT-based monitoring system to provide monitoring, assistance, and stimulation to older adults living alone in their own houses. The creation of an Internet of Robotics Things (IoRT) based on the interplay between pervasive smart objects and autonomous robotic systems is claimed to enable the creation of innovative services conceived for assisting the final user, especially in elderly care. The synergy between IoT and a Socially Assistive Robot (SAR) was conceived to offer robustness, reconfiguration, heterogeneity, and scalability, by bringing a strong added value to both the current SAR and IoT technologies. First, we propose a method to achieve the synergy and integration between the IoT system and the robot; then, we show how our method increases the performance and effectiveness of both to provide long-term support to the older adults. To do so, we present a case-study, where we focus on the detection of signs of the frailty syndrome, a set of vulnerabilities typically conveyed by a cognitive and physical decline in older people that concur in amplifying the risks of major diseases hindering the capabilities of independent living. Experimental evaluation is performed in both controlled settings and in a long-term real-world pilot study with 9 older adults in their own apartments, where the system was deployed autonomously for, on average, 12 weeks.
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| 7. |
- Luperto, Matteo, et al.
(författare)
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User feedback and remote supervision for assisted living with mobile robots : A field study in long-term autonomy
- 2022
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Ingår i: Robotics and Autonomous Systems. - : Elsevier. - 0921-8890 .- 1872-793X. ; 155
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Tidskriftsartikel (refereegranskat)abstract
- In an ageing society, the at-home use of Socially Assistive Robots (SARs) could provide remote monitoring of their users' well-being, together with physical and psychological support. However, private home environments are particularly challenging for SARs, due to their unstructured and dynamic nature which often contributes to robots' failures. For this reason, even though several prototypes of SARs for elderly care have been developed, their commercialisation and wide-spread at-home use are yet to be effective. In this paper, we analyse how including the end users' feedback impacts the SARs reliability and acceptance. To do so, we introduce a Monitoring and Logging System (MLS) for remote supervision, which increases the explainability of SAR-based systems deployed in older adults' apartments, while also allowing the exchange of feedback between caregivers, technicians, and older adults. We then present an extensive field study showing how long-term deployment of autonomous SARs can be accomplished by relying on such a feedback loop to address any potential issue. To this end, we provide the results obtained in a 130-week long study where autonomous SARs were deployed in the apartments of 10 older adults, with the aim of possibly serving and assisting future practitioners, with the knowledge collected from this extensive experimental campaign, to fill the gap that currently exists for the widespread adoption of SARs.
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| 8. |
- Monroy, Javier G., et al.
(författare)
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Calibration of mox gas sensors in open sampling systems based on gaussian processes
- 2012
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Ingår i: Proceedings of the IEEE Sensors Conference, 2012. - : IEEE conference proceedings. - 9781457717659 ; , s. 1-4
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Konferensbidrag (refereegranskat)abstract
- Calibration of metal oxide (MOX) gas sensor for continuous monitoring is a complex problem due to the highly dynamic characteristics of the gas sensor signal when exposed to natural environment (Open Sampling System - OSS). This work presents a probabilistic approach to the calibration of a MOX gas sensor based on Gaussian Processes (GP). The proposed approach estimates for every sensor measurement a probability distribution of the gas concentration. This enables the calculation of confidence intervals for the predicted concentrations. This is particularly important since exact calibration is hard to obtain due to the chaotic nature that dominates gas dispersal. The proposed approach has been tested with an experimental setup where an array of MOX sensors and a Photo Ionization Detector (PID) are placed downwind w.r.t. the gas source. The PID is used to obtain ground truth concentration. Comparison with standard calibration methods demonstrates the advantage of the proposed approach.
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| 9. |
- Monroy, Javier, et al.
(författare)
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GADEN : A 3D Gas Dispersion Simulator for Mobile Robot Olfaction in Realistic Environments
- 2017
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Ingår i: Sensors. - Basel, Switzerland : MPDI AG. - 1424-8220. ; 17:7, s. 1479-1494
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Tidskriftsartikel (refereegranskat)abstract
- This work presents a simulation framework developed under the widely used Robot Operating System (ROS) to enable the validation of robotics systems and gas sensing algorithms under realistic environments. The framework is rooted in the principles of computational fluid dynamics and filament dispersion theory, modeling wind flow and gas dispersion in 3D real-world scenarios (i.e., accounting for walls, furniture, etc.). Moreover, it integrates the simulation of different environmental sensors, such as metal oxide gas sensors, photo ionization detectors, or anemometers. We illustrate the potential and applicability of the proposed tool by presenting a simulation case in a complex and realistic office-like environment where gas leaks of different chemicals occur simultaneously. Furthermore, we accomplish quantitative and qualitative validation by comparing our simulated results against real-world data recorded inside a wind tunnel where methane was released under different wind flow profiles. Based on these results, we conclude that our simulation framework can provide a good approximation to real world measurements when advective airflows are present in the environment.
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| 10. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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