Charting the dynamics of translation

Codon usage bias (CUB) is the well-known phenomenon that the frequency of synonymous codons is unequal. This is presumably the result of adaptive pressures favouring some codons over others. The underlying reason for this pressure is unknown, although a large number of possible driver mechanisms have been proposed. According to one hypothesis, the decoding time could be such a driver. A tacit assumption of this hypothesis is that faster codons lead to a higher translation rate which in turn is more resource efficient. While it is generally assumed that there is such a link, there are no rigorous studies to establish under which conditions the link between translation speed and rate actually exists. Using a computational simulation model and explicitly calculated codon decoding times, this contribution maps the entire range of dynamical regimes of translation. These simulations make it possible to understand precisely under which conditions translation speed and rate are linked

Geometric deep learning: going beyond Euclidean data

Many scientific fields study data with an underlying structure that is a non-Euclidean space. Some examples include social networks in computational social sciences, sensor networks in communications, functional networks in brain imaging, regulatory networks in genetics, and meshed surfaces in computer graphics. In many applications, such geometric data are large and complex (in the case of social networks, on the scale of billions), and are natural targets for machine learning techniques. In particular, we would like to use deep neural networks, which have recently proven to be powerful tools for a broad range of problems from computer vision, natural language processing, and audio analysis. However, these tools have been most successful on data with an underlying Euclidean or grid-like structure, and in cases where the invariances of these structures are built into networks used to model them. Geometric deep learning is an umbrella term for emerging techniques attempting to generalize (structured) deep neural models to non-Euclidean domains such as graphs and manifolds. The purpose of this paper is to overview different examples of geometric deep learning problems and present available solutions, key difficulties, applications, and future research directions in this nascent field

Evolutionary pressures on the yeast transcriptome

Codon usage bias (CUB) is the well known phenomenon that the frequency of synonymous codons is unequal. This is presumably the result of adaptive pressures favouring some codons over others. The underlying reason for this pressure is unknown, although a large number of possible driver mechanisms have been proposed; one of them is the decoding time. The standard model to calculate decoding time is the Gromadski- Rodnina model. Yet, recently, there have been a number of studies arguing to the effect that this conventional speed-model is not relevant to understand the dynamics of translation. However, results remain inconclusive so far. This contribution takes a novel approach to address this issue based on comparing mRNA with random synonymous variants to estimate the evolutionary pressures that have acted on the transcriptome. It emerges that over 70%of ORFs have been subject to a strong selection pressure for translation speed and that there is also a strong selection pressure for the avoidance of traffic jams. Finally, it is also shown that both homogeneous and very heterogeneous transcripts are over-represented. These results corroborate the validity of the Gromadski-Rodnina model

Simulation Genres and Student Uptake: The Patient Health Record in Clinical Nursing Simulations

Drawing on fieldwork, this article examines nursing students’ design and use of a patient health record during clinical simulations, where small teams of students provide nursing care for a robotic patient. The student-designed patient health record provides a compelling example of how simulation genres can both authentically coordinate action within a classroom simulation and support professional genre uptake. First, the range of rhetorical choices available to students in designing their simulation health records are discussed. Then, the article draws on an extended example of how student uptake of the patient health record within a clinical simulation emphasized its intertextual relationship to other genres, its role mediating social interactions with the patient and other providers, and its coordination of embodied actions. Connections to students’ experiences with professional genres are addressed throughout. The article concludes by considering initial implications of this research for disciplinary and professional writing courses

Consciousness, Naturalism, and Human Flourishing

This chapter pursues the question of naturalism in the context of non-Western philosophical contributions to ethics and philosophy of mind: First, what conception of naturalism, if any, is best suited to capture the scope of Buddhist Reductionism? Second, can such a conception still accommodate the distinctive features of phenomenal consciousness (e.g., subjectivity, intentionality, first-person givenness, etc.). The first section reviews dominant conceptions of naturalism, and their applicability to the Buddhist project. In the second section, the author provides an example of problematic issues more stringent conceptions of naturalism under the guise of neurophysicalism confront, and evaluate Flanagan’s response to these issues. The third section considers briefly the reflexivity thesis (the thesis that consciousness consists in conscious mental states being implicitly self-aware), specifically as articulated by Dignaga, Dharmakirti and their followers, and uses this thesis to articulate a conception of minimal agency as mineness that, the author argues, further challenges Flanagan’s neurophysicalism stance and his compatibilist account of moral agency. The paper concludes, in the fourth section, by suggesting a way in which no-ownership conceptions of reflexive self-consciousness can help us both to get the structure of phenomenal consciousness right and to ground our conceptions of agency, intentionality, and moral responsibility

The [Not So] Hidden Curriculum of the Legalist State in the Book of Lord Shang and the Han-Fei-Zi

This paper loosely draws some parallels between the experience of a subject in a so-called “Legalist” state with that of a contemporary student in Western schooling today. I explore how governance in the Book of Lord Shang and the Hanfeizi can be interpreted as pedagogy. Defining pedagogy in a relatively broad sense, I investigate the rationalizations for the existence of the state, the application of state mechanisms, and even the concentration of the ruler’s power all teach subjects habits, attitudes, and sensibilities in a similar fashion to what Philip Jackson called the “hidden curriculum”. Through his framework of “crowds, praise, and power” this paper will explore how governance teaches and what those subjected to it learn. This study also attempts to provide some insight into the usefulness of approaching “Legalist” texts with a positive sociological lens

Textual Mediation in Simulated Nursing Handoffs: Examining How Student Writing Coordinates Action

In clinical nursing simulations, a group of students provide care for a robotic patient during a structured scenario. As care is transferred from one group to another, they participate in a patient handoff, with outgoing students passing key information onto incoming students. In healthcare, the nursing handoff is a critical and perilous communication moment that is mediated by a range of participants and texts. Drawing on observations and video recordings of 52 simulation handoffs in the United States, this article examines how two student-designed texts – a collaborative patient chart and individual notes – are leveraged during the handoff. I also consider how handoff talk and writing changes as student nursing knowledge increases over the course of a year. By focusing on textual mediation of the simulated nursing handoff, this article contributes to existing research on professional writing pedagogy and to nursing scholarship on the handoff. Ultimately, it argues that a textual mediation framework can help bridge class room and professional contexts by evaluating student writing not for how successfully it meets a set of imposed criteria but for how effectively it supports classroom activities