Centering inclusivity in the design of online conferences: An OHBM-Open Science perspective

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume

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, 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 fl ux 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, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost 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 fi eld 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 delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so 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 autophagy assays, we hope to encourage technical innovation in the field

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

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

Influence of the repetition rate and pulse duration on the incubation effect in multiple-shots ultrafast laser ablation of steel

AbstractWe report on an experimental study of the incubation effect during laser ablation of stainless steel with fs- and ps-pulses at high repetition rates. Ablation thresholds for multiple pulses N have been estimated. As expected, the ablation threshold decreases with N due to damage accumulation. The related incubation coefficient has been determined at different repetition rates, from 50-kHz to 1-MHz and two pulse durations: 650-fs and 10-ps. Results show that the incubation effect is lower for fs-pulses below 600kHz. At higher repetition rates incubation is more pronounced regardless of the pulse duration, probably due to heat accumulation

Real time ablation rate measurement during high aspect-ratio hole drilling with a 120-ps fiber laser

We report on the instantaneous detection of the ablation rate as a function of depth during ultrafast microdrilling of metal targets. The displacement of the ablation front has been measured with a sub-wavelength resolution using an all-optical sensor based on the laser diode self-mixing interferometry. The time dependence of the laser ablation process within the depth of aluminum and stainless steel targets has been investigated to study the evolution of the material removal rate in high aspect-ratio micromachined holes. (C)2011 Optical Society of Americ

Influence of the Repetition Rate and Pulse Duration on the Incubation Effect in Multiple-Shots Ultrafast Laser Ablation of Steel

AbstractWe report on an experimental study of the incubation effect during laser ablation of stainless steel with fs- and ps-pulses at high repetition rates. Ablation thresholds for multiple pulses N have been estimated. As expected, the ablation threshold decreases with N due to damage accumulation. The related incubation coefficient has been determined at different repetition rates, from 50-kHz to 1-MHz and two pulse durations: 650-fs and 10-ps. Results show that the incubation effect is lower for fs-pulses below 600kHz. At higher repetition rates incubation is more pronounced regardless of the pulse duration, probably due to heat accumulation

Direct investigation of the ablation rate evolution during laser drilling of high aspect ratio micro-holes

The recent development of ultrafast laser ablation technology in precision micromachining has dramatically increased the demand for reliable and real-time detection systems to characterize the material removal process. In particular, the laser percussion drilling of metals is lacking of non-invasive techniques able to monitor into the depth the spatial-and time-dependent evolution all through the ablation process. To understand the physical interaction between bulk material and high-energy light beam, accurate in-situ measurements of process parameters such as the penetration depth and the removal rate are crucial. We report on direct real time measurements of the ablation front displacement and the removal rate during ultrafast laser percussion drilling of metals by implementing a contactless sensing technique based on optical feedback interferometry. High aspect ratio micro-holes were drilled onto steel plates with different thermal properties (AISI 1095 and AISI 301) and Aluminum samples using 120-ps/110-kHz pulses delivered by a microchip laser fiber amplifier. Percussion drilling experiments have been performed by coaxially aligning the diode laser probe beam with the ablating laser. The displacement of the penetration front was instantaneously measured during the process with a resolution of 0.41 mu m by analyzing the sawtooth-like induced modulation of the interferometric signal out of the detector system