The Quaking RNA-binding proteins as regulators of cell differentiation

First published: 17 March 2022The RNA-binding protein Quaking (QKI) has emerged as a potent regulator of cellular differentiation in developmental and pathological processes. The QKI gene is itself alternatively spliced to produce three major isoforms, QKI-5, QKI-6, and QKI-7, that possess very distinct functions. Here, we highlight roles of the different QKI isoforms in neuronal, vascular, muscle, and monocyte cell differentiation, and during epithelial-mesenchymal transition in cancer progression. QKI isoforms control cell differentiation through regulating alternative splicing, mRNA stability and translation, with activities in gene transcription now also becoming evident. These diverse functions of the QKI isoforms contribute to their broad influences on RNA metabolism and cellular differentiation. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Development.Daniel P. Neumann, Gregory J. Goodall, Philip A. Gregor

Localization dynamics in a binary two-dimensional cellular automaton: the Diffusion Rule

We study a two-dimensional cellular automaton (CA), called Diffusion Rule (DR), which exhibits diffusion-like dynamics of propagating patterns. In computational experiments we discover a wide range of mobile and stationary localizations (gliders, oscillators, glider guns, puffer trains, etc), analyze spatio-temporal dynamics of collisions between localizations, and discuss possible applications in unconventional computing.Comment: Accepted to Journal of Cellular Automat

Absence of lattice strain anomalies at the electronic topological transition in zinc at high pressure

High pressure structural distortions of the hexagonal close packed (hcp) element zinc have been a subject of controversy. Earlier experimental results and theory showed a large anomaly in lattice strain with compression in zinc at about 10 GPa which was explained theoretically by a change in Fermi surface topology. Later hydrostatic experiments showed no such anomaly, resulting in a discrepancy between theory and experiment. We have computed the compression and lattice strain of hcp zinc over a wide range of compressions using the linearized augmented plane wave (LAPW) method paying special attention to k-point convergence. We find that the behavior of the lattice strain is strongly dependent on k-point sampling, and with large k-point sets the previously computed anomaly in lattice parameters under compression disappears, in agreement with recent experiments.Comment: 9 pages, 6 figures, Phys. Rev. B (in press

Feedback Vertex Sets in Tournaments

We study combinatorial and algorithmic questions around minimal feedback vertex sets in tournament graphs. On the combinatorial side, we derive strong upper and lower bounds on the maximum number of minimal feedback vertex sets in an n-vertex tournament. We prove that every tournament on n vertices has at most 1.6740^n minimal feedback vertex sets, and that there is an infinite family of tournaments, all having at least 1.5448^n minimal feedback vertex sets. This improves and extends the bounds of Moon (1971). On the algorithmic side, we design the first polynomial space algorithm that enumerates the minimal feedback vertex sets of a tournament with polynomial delay. The combination of our results yields the fastest known algorithm for finding a minimum size feedback vertex set in a tournament

Higgs Bundles, Gauge Theories and Quantum Groups

The appearance of the Bethe Ansatz equation for the Nonlinear Schr\"{o}dinger equation in the equivariant integration over the moduli space of Higgs bundles is revisited. We argue that the wave functions of the corresponding two-dimensional topological U(N) gauge theory reproduce quantum wave functions of the Nonlinear Schr\"{o}dinger equation in the $N$-particle sector. This implies the full equivalence between the above gauge theory and the $N$-particle sub-sector of the quantum theory of Nonlinear Schr\"{o}dinger equation. This also implies the explicit correspondence between the gauge theory and the representation theory of degenerate double affine Hecke algebra. We propose similar construction based on the $G/G$ gauged WZW model leading to the representation theory of the double affine Hecke algebra. The relation with the Nahm transform and the geometric Langlands correspondence is briefly discussed.Comment: 48 pages, typos corrected, one reference adde

Asymptomatic Infant Rib Fractures Are Primarily Non-abuse-Related and Should Not Be Used to Assess Physical Child Abuse

Finding infant rib fractures was for many years an almost undisputed proof that physical child abuse took place. Yet, these rib fractures are virtually always occult and asymptomatic and are only identified when looked for, usually with X-rays, from physical child abuse accusations related to, e.g., suspicion of the shaken baby syndrome. In a recent systematic literature review (searched in Cochran, Embase, PubMed and Sociological Abstracts), Güvensel questioned the diagnostic accuracy of rib fractures to be caused by abuse, due to lack of sufficient scientific evidence. Further, there is currently a world-wide disagreement between physicians considering themselves child abuse specialized, and physicians that explore non-abuse-related symptoms that may mimic physical abuse, which, it is hoped, will significantly reduce current unjustified child abuse diagnoses. In an attempt to help resolving this disagreement, we hypothesize that the probability of physical child abuse-related infant rib fractures is significantly lower than the probability of all other possible non-abuse-related causes of occult asymptomatic infant rib fractures, e.g., from birth trauma, prematurity, osteogenesis imperfecta, hypermobile Ehlers-Danlos Syndrome, severe chronic placental pathology (e.g., massive perivillous fibrin depositions and severe chronic histiocytic intervillositis), and vitamin-D deficiency. As method, we attempted to assess the incidence of these various causes of infant rib fractures, in the Netherlands and the USA. The results are that the estimated Dutch and USA physical abuse-related infant rib fracture incidences are at least about 250 and 45 times lower than the sum of all the non-abuse-related estimates. Because these latter rib fractures are occult and asymptomatic, it is likely that (many) more could be out there. In conclusion, occult asymptomatic rib fractures develop perinatally, virtually always as birth trauma, in infants with sufficiently weak bones due to vitamin D deficiency, transmitted by their vitamin D deficient pregnant mothers. This group also includes cortical rib cracks due to deformation forces, with an estimated 186/100,000 incidence. And, despite obvious uncertainties in all estimated incidences, we provided strong evidence that our hypothesis has relevance, implying that the abundant occult asymptomatic rib fractures, when found in infants, should not be used to assess potential physical child abuse

Production of Medical Radioisotopes with High Specific Activity in Photonuclear Reactions with γ\gamma Beams of High Intensity and Large Brilliance

We study the production of radioisotopes for nuclear medicine in $(\gamma,x{\rm n}+y{\rm p})$ photonuclear reactions or ($\gamma,\gamma'$) photoexcitation reactions with high flux [($10^{13}-10^{15}$)$\gamma$/s], small diameter $\sim (100 \, \mu$m$)^2$ and small band width ($\Delta E/E \approx 10^{-3}-10^{-4}$) $\gamma$ beams produced by Compton back-scattering of laser light from relativistic brilliant electron beams. We compare them to (ion,$x$n$+ y$p) reactions with (ion=p,d,$\alpha$) from particle accelerators like cyclotrons and (n,$\gamma$) or (n,f) reactions from nuclear reactors. For photonuclear reactions with a narrow $\gamma$ beam the energy deposition in the target can be managed by using a stack of thin target foils or wires, hence avoiding direct stopping of the Compton and pair electrons (positrons). $(\gamma,\gamma')$ isomer production via specially selected $\gamma$ cascades allows to produce high specific activity in multiple excitations, where no back-pumping of the isomer to the ground state occurs. We discuss in detail many specific radioisotopes for diagnostics and therapy applications. Photonuclear reactions with $\gamma$ beams allow to produce certain radioisotopes, e.g. $^{47}$Sc, $^{44}$Ti, $^{67}$Cu, $^{103}$Pd, $^{117m}$Sn, $^{169}$Er, $^{195m}$Pt or $^{225}$Ac, with higher specific activity and/or more economically than with classical methods. This will open the way for completely new clinical applications of radioisotopes. For example $^{195m}$Pt could be used to verify the patient's response to chemotherapy with platinum compounds before a complete treatment is performed. Also innovative isotopes like $^{47}$Sc, $^{67}$Cu and $^{225}$Ac could be produced for the first time in sufficient quantities for large-scale application in targeted radionuclide therapy.Comment: submitted to Appl. Phys.

Environment-Induced Decoherence and the Transition From Quantum to Classical

We study dynamics of quantum open systems, paying special attention to those aspects of their evolution which are relevant to the transition from quantum to classical. We begin with a discussion of the conditional dynamics of simple systems. The resulting models are straightforward but suffice to illustrate basic physical ideas behind quantum measurements and decoherence. To discuss decoherence and environment-induced superselection einselection in a more general setting, we sketch perturbative as well as exact derivations of several master equations valid for various systems. Using these equations we study einselection employing the general strategy of the predictability sieve. Assumptions that are usually made in the discussion of decoherence are critically reexamined along with the ``standard lore'' to which they lead. Restoration of quantum-classical correspondence in systems that are classically chaotic is discussed. The dynamical second law -it is shown- can be traced to the same phenomena that allow for the restoration of the correspondence principle in decohering chaotic systems (where it is otherwise lost on a very short time-scale). Quantum error correction is discussed as an example of an anti-decoherence strategy. Implications of decoherence and einselection for the interpretation of quantum theory are briefly pointed out.Comment: 80 pages, 7 figures included, Lectures given by both authors at the 72nd Les Houches Summer School on "Coherent Matter Waves", July-August 199

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results