Visual scanning as a reference framework for interactive representation design

International audienceWhen designing a representation, the designer implicitly formulates a sequence of visual tasks required to understand and use the representation effectively. This paper aims at making the sequence of visual tasks explicit in order to help designers elicit their design choices. In particular, we present a set of concepts to systematically analyse what a user must theoretically do to decipher representations. The analysis consists of a decomposition of the activity of scanning into elementary visualization operations. We show how the analysis applies to various existing representations, and how expected benefits can be expressed in terms of elementary operations. The set of elementary operations form the basis of a shared language for representation designers. The decomposition highlights the challenges encountered by a user when deciphering a representation and helps designers to exhibit possible flaws in their design, justify their choices, and compare designs. We also show that interaction with a representation can be considered as facilitation to perform the elementary operations

Observational consequences of fine structure line optical depths on infrared spectral diagnostics

It has long been known that infrared fine structure lines of abundant ions, like the [O III] 88 micron line, can become optically thick in H II regions under certain high luminosity conditions. This could mitigate their potential as diagnostic tools, especially if the source is too dusty for optical spectroscopy to otherwise determine the system's parameters. We examined a series of photoionization calculations which were designed to push the nebulae into the limit where many IR lines should be quite optically thick. We find that radiative transfer effects do not significantly change the observed emission line spectrum. This is due to a combination of grain absorption of the hydrogen ionizing continuum and the fact that the correction for stimulated emission in these lines is large. Given these results, and the likelihood that real objects have non-thermal line broadening, it seems unlikely that line optical depth presents a problem in using these lines as diagnostics of the physical conditions or chemical composition.Comment: 16 pages, 4 figures, to be published in the February 2003 issue of the PAS

Merleau-Ponty and the Measuring Body

In recent years a growing number of scholars in science studies and related fields are developing new ontologies to displace entrenched dualisms. These efforts often go together with a renewed interest in the roles played by symbolisms and tools in knowledge and being. This article brings Maurice Merleau-Ponty into these conversations, positioning him as a precursor of today’s innovative recastings of technoscience. While Merleau-Ponty is often invoked in relation to his early work on the body and embodiment, this article focuses on his later work, where the investigation of perception is integrated with an ontological exploration. The resulting approach revolves around the highly original idea of the body as a standard of measurement. We further develop this idea by coining the term ‘the measuring body’, which to a greater extent than did Merleau-Ponty accentuates the relative autonomy of symbolisms and tools and their capacity to decentre the perceiving body

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling

Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 angstrom cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two a-helices connected by an a-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50-55 angstrom of the exit tunnel. The structure reveals how a-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome

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