There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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.

For example, 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 versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase 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. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy.

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. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. 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 assays, we hope to encourage technical innovation in the field.

/pdf/guidelines-for-the-use-and-interpretation-of-assays-for-ijf2t30pbq.pdf

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

http://academic.oup.com/auk/article-pdf/102/3/661/30080634/auk0661.pdf

Scaling: why is animal size so important?

Technological advancements have led to the development of numerous wearable robotic devices for the physical assistance and restoration of human locomotion. While many challenges remain with respect to the mechanical design of such devices, it is at least equally challenging and important to develop strategies to control them in concert with the intentions of the user. This work reviews the state-of-the-art techniques for controlling portable active lower limb prosthetic and orthotic (P/O) devices in the context of locomotive activities of daily living (ADL), and considers how these can be interfaced with the user’s sensory-motor control system. This review underscores the practical challenges and opportunities associated with P/O control, which can be used to accelerate future developments in this field. Furthermore, this work provides a classification scheme for the comparison of the various control strategies. As a novel contribution, a general framework for the control of portable gait-assistance devices is proposed. This framework accounts for the physical and informatic interactions between the controller, the user, the environment, and the mechanical device itself. Such a treatment of P/Os – not as independent devices, but as actors within an ecosystem – is suggested to be necessary to structure the next generation of intelligent and multifunctional controllers. Each element of the proposed framework is discussed with respect to the role that it plays in the assistance of locomotion, along with how its states can be sensed as inputs to the controller. The reviewed controllers are shown to fit within different levels of a hierarchical scheme, which loosely resembles the structure and functionality of the nominal human central nervous system (CNS). Active and passive safety mechanisms are considered to be central aspects underlying all of P/O design and control, and are shown to be critical for regulatory approval of such devices for real-world use. The works discussed herein provide evidence that, while we are getting ever closer, significant challenges still exist for the development of controllers for portable powered P/O devices that can seamlessly integrate with the user’s neuromusculoskeletal system and are practical for use in locomotive ADL.

/pdf/control-strategies-for-active-lower-extremity-prosthetics-5ojhkwsifh.pdf

Control strategies for active lower extremity prosthetics and orthotics: a review

The planar bipedal testbed MABEL contains springs in its drivetrain for the purpose of enhancing both energy efficiency and agility of dynamic locomotion. While the potential energetic benefits of springs are well documented in the literature, feedback control designs that effectively realize this potential are lacking. In this paper, we extend and apply the methods of virtual constraints and hybrid zero dynamics, originally developed for rigid robots with a single degree of underactuation, to MABEL, a bipedal walker with a novel compliant transmission and multiple degrees of underactuation. A time-invariant feedback controller is designed such that the closed-loop system respects the natural compliance of the open-loop system and realizes exponentially stable walking gaits. Five experiments are presented that highlight different aspects of MABEL and the feedback design method, ranging from basic elements such as stable walking and robustness under perturbations, to energy efficiency and a walking speed of 1.5âmâsâ1 (3.4âmph). The experiments also compare two feedback implementations of the virtual constraints, one based on PD control of Westervelt et al., and a second that implements a full hybrid zero dynamics controller. On MABEL, the full hybrid zero dynamics controller yields a much more faithful realization of the desired virtual constraints and was instrumental in achieving more rapid walking.

/pdf/a-compliant-hybrid-zero-dynamics-controller-for-stable-2qy7d6sdzn.pdf

A Compliant Hybrid Zero Dynamics Controller for Stable, Efficient and Fast Bipedal Walking on MABEL

This paper presents the design and implementation of a bounding controller for the MIT Cheetah 2 and its experimental results. The paper introduces the architecture of the controller along with the...

https://journals.sagepub.com/doi/pdf/10.1177/0278364917694244

High-speed bounding with the MIT Cheetah 2: Control design and experiments

This paper introduces MABEL, a new platform for the study of bipedal locomotion in robots. One of the purposes of building the mechanism is to explore a novel powertrain design that incorporates compliance, with the objective of improving the power efficiency of the robot, both in steady state operation and in responding to disturbances. A second purpose is to inspire the development of new feedback control algorithms for running on level surfaces and walking on rough terrain. A third motivation for building the robot is science and technology outreach; indeed, it is already included in tours when K-through-12 students visit the College of Engineering at the University of Michigan. MABEL is currently walking at 1.1 m/s on a level surface, and a related monopod at Carnegie Mellon is hopping well, establishing that the testbed has the potential to realize its many objectives.

/pdf/mabel-a-new-robotic-bipedal-walker-and-runner-1nbb06i9ba.pdf

MABEL, a new robotic bipedal walker and runner

A mathematical formalism for designing running gaits in bipedal robots with compliance is introduced and subsequently validated experimentally on MABEL, a planar biped that contains springs in its drivetrain. The methods of virtual constraints and hybrid zero dynamics are used to design a time-invariant feedback controller that respects the natural compliance of the open-loop system. In addition, it also enables active force control within the compliant hybrid zero dynamics allowing within-stride adjustments of the effective stance leg stiffness. The proposed control strategy was implemented on and resulted in a kneed-biped running record of 3.06 m/s (10.9 kph or 6.8 mph).

http://research.me.udel.edu/~poulakas/Publications/papers/IJRR_Running_Paper_sub.pdf

Embedding active force control within the compliant hybrid zero dynamics to achieve stable, fast running on MABEL

United States. Defense Advanced Research Projects Agency. Maximum Mobility and Manipulation (M3) Program

http://www.roboticsproceedings.org/rss11/p47.pdf

Hae-Won Park

Papers

A Compliant Hybrid Zero Dynamics Controller for Stable, Efficient and Fast Bipedal Walking on MABEL

High-speed bounding with the MIT Cheetah 2: Control design and experiments

MABEL, a new robotic bipedal walker and runner

Embedding active force control within the compliant hybrid zero dynamics to achieve stable, fast running on MABEL

Online planning for autonomous running jumps over obstacles in high-speed quadrupeds