From symbiont to parasite: the evolution of for-profit science publishing.

Two 17th century institutions-learned societies and scientific journals-transformed science in ways that still dominate our professional lives today. Learned societies like the American Society for Cell Biology remain relevant because they provide forums for sharing results, discussing the practice of science, and projecting our voices to the public and the policy makers. Scientific journals still disseminate our work, but in the Internet-connected world of the 21st century, this is no longer their critical function. Journals remain relevant almost entirely because they provide a playing field for scientific and professional competition: to claim credit for a discovery, we publish it in a peer-reviewed journal; to get a job in academia or money to run a lab, we present these published papers to universities and funding agencies. Publishing is so embedded in the practice of science that whoever controls the journals controls access to the entire profession. We must reform our methods for evaluating the contributions of younger scientists and deflate the power of a small number of "elite" journals. More generally, given the recent failure of research institutions around the world to strike satisfactory deals with publishing giant Elsevier, the time has come to examine the motives and methods of those to whom we have entrusted the keys to the kingdom of science

tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay.

Yeast tRNA ligase (Trl1) is an essential trifunctional enzyme that catalyzes exon-exon ligation during tRNA biogenesis and the non-conventional splicing of HAC1 mRNA during the unfolded protein response (UPR). The UPR regulates the protein folding capacity of the endoplasmic reticulum (ER). ER stress activates Ire1, an ER-resident kinase/RNase, which excises an intron from HAC1 mRNA followed by exon-exon ligation by Trl1. The spliced product encodes for a potent transcription factor that drives the UPR. Here we report the crystal structure of Trl1 RNA ligase domain from Chaetomium thermophilum at 1.9 Å resolution. Structure-based mutational analyses uncovered kinetic competition between RNA ligation and degradation during HAC1 mRNA splicing. Incompletely processed HAC1 mRNA is degraded by Xrn1 and the Ski/exosome complex. We establish cleaved HAC1 mRNA as endogenous substrate for ribosome-associated quality control. We conclude that mRNA decay and surveillance mechanisms collaborate in achieving fidelity of non-conventional mRNA splicing during the UPR

Unsupervised Discovery of Phonological Categories through Supervised Learning of Morphological Rules

We describe a case study in the application of {\em symbolic machine learning} techniques for the discovery of linguistic rules and categories. A supervised rule induction algorithm is used to learn to predict the correct diminutive suffix given the phonological representation of Dutch nouns. The system produces rules which are comparable to rules proposed by linguists. Furthermore, in the process of learning this morphological task, the phonemes used are grouped into phonologically relevant categories. We discuss the relevance of our method for linguistics and language technology

Static and dynamical properties of a supercooled liquid confined in a pore

We present the results of a Molecular Dynamics computer simulation of a binary Lennard-Jones liquid confined in a narrow pore. The surface of the pore has an amorphous structure similar to that of the confined liquid. We find that the static properties of the liquid are not affected by the confinement, while the dynamics changes dramatically. By investigating the time and temperature dependence of the intermediate scattering function we show that the dynamics of the particles close to the center of the tube is similar to the one in the bulk, whereas the characteristic relaxation time tau_q(T,rho) of the intermediate scattering function at wavevector q and distance rho from the axis of the pore increases continuously when approaching the wall, leading to an apparent divergence in the vicinity of the wall. This effect is seen for intermediate temperatures down to temperatures close to the glass transition. The rho-dependence of tau_q(T,rho) can be described by an empirical law of the form tau_q(T,\rho)=f_q(T) exp [Delta_q/(rho_p-rho)], where Delta_q and \rho_q are constants, and f_q(T) is the only parameter which shows a significant temperature dependence.Comment: 4 pages of Latex, 4 figures Pari

The relaxation dynamics of a supercooled liquid confined by rough walls

We present the results of molecular dynamics computer simulations of a binary Lennard-Jones liquid confined between two parallel rough walls. These walls are realized by frozen amorphous configurations of the same liquid and therefore the structural properties of the confined fluid are identical to the ones of the bulk system. Hence this setup allows us to study how the relaxation dynamics is affected by the pure effect of confinement, i.e. if structural changes are completely avoided. We find that the local relaxation dynamics is a strong function of z, the distance of the particles from the wall, and that close to the surface the typical relaxation times are orders of magnitude larger than the ones in the bulk. Because of the cooperative nature of the particle dynamics, the slow dynamics also affects the dynamics of the particles for large values of z. Using various empirical laws, we are able to parameterize accurately the z-dependence of the generalized incoherent intermediate scattering function F_s(q,z,t) and also the spatial dependence of structural relaxation times. These laws allow us to determine various dynamical length scales and we find that their temperature dependence is compatible with an Arrhenius law. Furthermore, we find that at low temperatures time and space dependent correlation function fulfill a generalized factorization property similar to the one predicted by mode-coupling theory for bulk systems. For thin films and/or at sufficiently low temperatures, we find that the relaxation dynamics is influenced by the two walls in a strongly non-linear way in that the slowing down is much stronger than the one expected from the presence of only one confining wall. ....Comment: 22 pages of Late