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

Large-N Solution of the Heterotic Weighted Non-Linear Sigma-Model

We study a heterotic two-dimensional N=(0,2) gauged non-linear sigma-model whose target space is a weighted complex projective space. We consider the case with N positively and N^~=N_F - N negatively charged fields. This model is believed to give a description of the low-energy physics of a non-Abelian semi-local vortex in a four-dimensional N=2 supersymmetric U(N) gauge theory with N_F > N matter hypermultiplets. The supersymmetry in the latter theory is broken down to N=1 by a mass term for the adjoint fields. We solve the model in the large-N approximation and explore a two-dimensional subset of the mass parameter space for which a discrete Z_{N-N^~} symmetry is preserved. Supersymmetry is generically broken, but it is preserved for special values of the masses where a new branch opens up and the model becomes super-conformal.Comment: 34 pages, 10 figures, references adde