| 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. |
- Chung, Michael Jae-Yoon, et al.
(författare)
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Autonomous Question Answering with Mobile Robots in Human-Populated Environments
- 2016
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Ingår i: Proceedings of the 2016 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS’16). - : IEEE.
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Konferensbidrag (refereegranskat)abstract
- Autonomous mobile robots will soon become ubiquitous in human-populated environments. Besides their typical applications in fetching, delivery, or escorting, such robots present the opportunity to assist human users in their daily tasks by gathering and reporting up-to-date knowledge about the environment. In this paper, we explore this use case and present an end-to-end framework that enables a mobile robot to answer natural language questions about the state of a large-scale, dynamic environment asked by the inhabitants of that environment. The system parses the question and estimates an initial viewpoint that is likely to contain information for answering the question based on prior environment knowledge. Then, it autonomously navigates towards the viewpoint while dynamically adapting to changes and new information. The output of the system is an image of the most relevant part of the environment that allows the user to obtain an answer to their question. We additionally demonstrate the benefits of a continuously operating information gathering robot by showing how the system can answer retrospective questions about the past state of the world using incidentally recorded sensory data. We evaluate our approach with a custom mobile robot deployed in a university building, with questions collected from occupants of the building. We demonstrate our system's ability to respond to these questions in different environmental conditions.
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| 3. |
- Chung, Michael Jae-Yoon, et al.
(författare)
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Designing Information Gathering Robots for Human-Populated Environments
- 2015
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Ingår i: Proceedings of the 2015 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS’15). - : IEEE.
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Konferensbidrag (refereegranskat)abstract
- Advances in mobile robotics have enabled robots that can autonomously operate in human-populated environments. Although primary tasks for such robots might be fetching, delivery, or escorting, they present an untapped potential as information gathering agents that can answer questions for the community of co-inhabitants. In this paper, we seek to better understand requirements for such information gathering robots (InfoBots) from the perspective of the user requesting the information. We present findings from two studies: (i) a user survey conducted in two office buildings and (ii) a 4-day long deployment in one of the buildings, during which inhabitants of the building could ask questions to an InfoBot through a web-based interface. These studies allow us to characterize the types of information that InfoBots can provide for their users.
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| 4. |
- Chung, Michael Jae-Yoon, et al.
(författare)
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Exploring the Potential of Information Gathering Robots
- 2015
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Ingår i: Proceedings of the 10th Annual ACM/IEEE International Conference on Human-Robot Interaction Extended Abstracts (HRI’15). - New York, NY, USA : ACM Digital Library.
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Konferensbidrag (refereegranskat)abstract
- Autonomous mobile robots equipped with a number of sensors will soon be ubiquitous in human populated environments. In this paper we present an initial exploration into the potential of using such robots for information gathering. We present findings from a formative user survey and a 4-day long Wizard-of-Oz deployment of a robot that answers questions such as "Is there free food on the kitchen table?" Our studies allow us to characterize the types of information that InfoBots might be most useful for.
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| 5. |
- Fox Franke, Daniel, et al.
(författare)
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Network Time Security for the Network Time Protocol
- 2020
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Rapport (refereegranskat)abstract
- This memo specifies Network Time Security (NTS), a mechanism for using Transport Layer Security (TLS) and Authenticated Encryption with Associated Data (AEAD) to provide cryptographic security for the client-server mode of the Network Time Protocol (NTP).NTS is structured as a suite of two loosely coupled sub-protocols. The first (NTS Key Establishment (NTS-KE)) handles initial authentication and key establishment over TLS. The second (NTS Extension Fields for NTPv4) handles encryption and authentication during NTP time synchronization via extension fields in the NTP packets, and holds all required state only on the client via opaque cookies.
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| 6. |
- Gonzalez-Ericsson, Paula, et al.
(författare)
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The path to a better biomarker: application of a risk management framework for the implementation of PD‐L1 and TILs as immuno‐oncology biomarkers into breast cancer clinical trials and daily practice
- 2020
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Ingår i: Journal of Pathology. - : Wiley. - 1096-9896 .- 0022-3417. ; 250:5, s. 667-684
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Forskningsöversikt (refereegranskat)abstract
- Immune checkpoint inhibitor therapies targeting PD‐1/PD‐L1 are now the standard of care in oncology across several hematologic and solid tumor types, including triple negative breast cancer (TNBC). Patients with metastatic or locally advanced TNBC with PD‐L1 expression on immune cells occupying ≥1% of tumor area demonstrated survival benefit with the addition of atezolizumab to nab‐paclitaxel. However, concerns regarding variability between immunohistochemical PD‐L1 assay performance and inter‐reader reproducibility have been raised. High tumor‐infiltrating lymphocytes (TILs) have also been associated with response to PD‐1/PD‐L1 inhibitors in patients with breast cancer (BC). TILs can be easily assessed on hematoxylin and eosin–stained slides and have shown reliable inter‐reader reproducibility. As an established prognostic factor in early stage TNBC, TILs are soon anticipated to be reported in daily practice in many pathology laboratories worldwide. Because TILs and PD‐L1 are parts of an immunological spectrum in BC, we propose the systematic implementation of combined PD‐L1 and TIL analyses as a more comprehensive immuno‐oncological biomarker for patient selection for PD‐1/PD‐L1 inhibition‐based therapy in patients with BC. Although practical and regulatory considerations differ by jurisdiction, the pathology community has the responsibility to patients to implement assays that lead to optimal patient selection. We propose herewith a risk‐management framework that may help mitigate the risks of suboptimal patient selection for immuno‐therapeutic approaches in clinical trials and daily practice based on combined TILs/PD‐L1 assessment in BC.
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| 7. |
- Lawrenson, Kate, et al.
(författare)
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Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk.
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| 8. |
- Lundell, Jens, et al.
(författare)
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Constrained Generative Sampling of 6-DoF Grasps
- 2023
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Ingår i: 2023 IEEE/RSJ International Conference on Intelligent Robots and Systems, IROS 2023. - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 2940-2946
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Konferensbidrag (refereegranskat)abstract
- Most state-of-the-art data-driven grasp sampling methods propose stable and collision-free grasps uniformly on the target object. For bin-picking, executing any of those reachable grasps is sufficient. However, for completing specific tasks, such as squeezing out liquid from a bottle, we want the grasp to be on a specific part of the object's body while avoiding other locations, such as the cap. This work presents a generative grasp sampling network, VCGS, capable of constrained 6-Degrees of Freedom (DoF) grasp sampling. In addition, we also curate a new dataset designed to train and evaluate methods for constrained grasping. The new dataset, called CONG, consists of over 14 million training samples of synthetically rendered point clouds and grasps at random target areas on 2889 objects. VCGS is benchmarked against GraspNet, a state-of-the-art unconstrained grasp sampler, in simulation and on a real robot. The results demonstrate that VCGS achieves a 10-15% higher grasp success rate than the baseline while being 2-3 times as sample efficient. Supplementary material is available on our project website.
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| 9. |
- Madry, Marianna, et al.
(författare)
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ST-HMP : Unsupervised Spatio-Temporal Feature Learning for Tactile Data
- 2014
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Ingår i: 2014 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION (ICRA). - : IEEE. ; , s. 2262-2269
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Konferensbidrag (refereegranskat)abstract
- Tactile sensing plays an important role in robot grasping and object recognition. In this work, we propose a new descriptor named Spatio-Temporal Hierarchical Matching Pursuit (ST-HMP) that captures properties of a time series of tactile sensor measurements. It is based on the concept of unsupervised hierarchical feature learning realized using sparse coding. The ST-HMP extracts rich spatio-temporal structures from raw tactile data without the need to predefine discriminative data characteristics. We apply it to two different applications: (1) grasp stability assessment and (2) object instance recognition, presenting its universal properties. An extensive evaluation on several synthetic and real datasets collected using the Schunk Dexterous, Schunk Parallel and iCub hands shows that our approach outperforms previously published results by a large margin.
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| 10. |
- Newbury, Rhys, et al.
(författare)
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Deep Learning Approaches to Grasp Synthesis: A Review
- 2023
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Ingår i: IEEE Transactions on robotics. - : Institute of Electrical and Electronics Engineers (IEEE). - 1552-3098 .- 1941-0468. ; 39:5, s. 3994-4015
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Tidskriftsartikel (refereegranskat)abstract
- Grasping is the process of picking up an object by applying forces and torques at a set of contacts. Recent advances in deep learning methods have allowed rapid progress in robotic object grasping. In this systematic review, we surveyed the publications over the last decade, with a particular interest in grasping an object using all six degrees of freedom of the end-effector pose. Our review found four common methodologies for robotic grasping: sampling-based approaches, direct regression, reinforcement learning, and exemplar approaches In addition, we found two 'supporting methods' around grasping that use deep learning to support the grasping process, shape approximation, and affordances. We have distilled the publications found in this systematic review (85 papers) into ten key takeaways we consider crucial for future robotic grasping and manipulation research.
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| 11. |
- Roh, Junha, et al.
(författare)
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Conditional Driving from Natural Language Instructions
- 2019
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Ingår i: Proceedings of the Conference on Robot Learning, CoRL 2019. - : ML Research Press. ; , s. 540-551
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Konferensbidrag (refereegranskat)abstract
- Widespread adoption of self-driving cars will depend not only on their safety but largely on their ability to interact with human users. Just like human drivers, self-driving cars will be expected to understand and safely follow natural-language directions that suddenly alter the pre-planned route according to user’s preference or in presence of ambiguities, particularly in locations with poor or outdated map coverage. To this end, we propose a language-grounded driving agent implementing a hierarchical policy using recurrent layers and gated attention. The hierarchical approach enables us to reason both in terms of high-level language instructions describing long time horizons and low-level, complex, continuous state/action spaces required for real-time control of a self-driving car. We train our policy with conditional imitation learning from realistic language data collected from human drivers and navigators. Through quantitative and interactive experiments within the CARLA framework, we show that our model can successfully interpret language instructions and follow them safely, even when generalizing to previously unseen environments. Code and video are available at: https://sites.google.com/view/language-grounded-driving.
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