A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

Ribosome profiling (Ribo-seq) has catalyzed a paradigm shift in our understanding of the translational vocabulary of the human genome, discovering thousands of translated open reading frames (ORFs) within long non-coding RNAs and presumed untranslated regions of protein-coding genes. However, reference gene annotation projects have been circumspect in their incorporation of these ORFs due to uncertainties about their experimental reproducibility and physiological roles. Yet, it is indisputable that certain Ribo-seq ORFs make stable proteins, others mediate gene regulation, and many have medical implications. Ultimately, the absence of standardized ORF annotation has created a circular problem: while Ribo-seq ORFs remain unannotated by reference biological databases, this lack of characterisation will thwart research efforts examining their roles. Here, we outline the initial stages of a community-led effort supported by GENCODE / Ensembl, HGNC and UniProt to produce a consolidated catalog of human Ribo-seq ORFs.

On Analysis

The understanding and acknowledgement of the problem of induction and its negative force on discourse failure bring intelligence studies towards a new theory of intelligence. The understanding of discourse failure opens a window to intelligence failure as a circular problem that intensifies itself by the human tendency to displace and redirect new knowledge that threatens orthodoxies, political assumptions and a uniform belief in nature. The result is that threats appearing in new variations will not easily be acknowledged or accepted, since they exist outside the normative threat paradigms and outside the existing language available to communicate threats that exist outside the possibilities of induction. The acknowledgement of this phenomenon discloses the problems that arise because intelligence has lacked a proper intelligence theory. It illustrates that if intelligence institutions want to reduce the damaging effect of the problem of induction and discourse fail- ure, and produce qualitative intelligence, they must probe beyond the limits of induction. A deep acknowledgement of the discourse failure theory therefore explains the reciprocal nature of intelli- gence, as well as capturing and identifying the circular dynamic between threats, threat perception and intelligence failure. This chapter examines how this phenomenon shapes intelligence analysis.

ON THE BIFURCATION AND CONTINUATION OF PERIODIC ORBITS IN THE THREE BODY PROBLEM

We consider the planar three body problem of planetary type and we study the generation and continuation of periodic orbits and mainly of asymmetric periodic orbits. Asymmetric orbits exist in the restricted circular three body problem only in particular resonances called "asymmetric resonances". However, numerical studies showed that in the general three body problem, asymmetric orbits may exist not only for asymmetric resonances, but for other kinds, too. In this work, we show the existence of asymmetric periodic orbits in the elliptic restricted problem. These families of periodic orbits continue existing and clarify the origin of many asymmetric periodic orbits in the general problem. Also, we illustrate how the families of periodic orbits of the restricted circular problem and those of the elliptic one join smoothly and form families in the general problem, verifying in this way the scenario first described by Bozis and Hadjidemetriou.