Integrating phylogenomics, phylogenetics, morphometrics, relative genome size and ecological niche modelling disentangles the diversification of Eurasian Euphorbia seguieriana s. l. (Euphorbiaceae)

Next generation sequencing has revolutionised biology. Restriction-associated DNA sequencing (RADseq) has primarily been used to study infraspecific relationships but has also been applied in multi-species phylogenomic analyses. In this study, we used a combination of phylogenomic (with RADseq data) and phylogenetic (with sequences of the nuclear internal transcribed spacer, ITS) methods to explore relationships within the taxonomically intricate Euphorbia seguieriana s. l., one of the most widespread Euphorbia taxa inhabiting zonal and extrazonal steppes from Iberia to Central Asia. In the inferred phylogenies the southeastern Balkan and Anatolian populations were clearly separated, supporting the distinction of E. niciciana from E. seguieriana at the species level. Within E. seguieriana, the populations from the Caucasus, Iran, and easternmost Anatolia were sister to all other populations based on RADseq, making necessary the description of a new, morphologically divergent subspecies, E. seguieriana subsp. armeniaca. Conversely, additional studies are needed to understand the status of E. seguieriana subsp. hohenackeri, which is sympatric with E. seguieriana subsp. armeniaca. Niche analyses indicated that differences in the climatic niche between E. niciciana and E. seguieriana are relatively small compared with the climatic differences between the regions over which they are distributed. Contrary to previous believes, E. niciciana and E. seguieriana are allopatric and have likely diverged during the Pleistocene in two different glacial refugia as suggested by distribution modelling. Euphorbia niciciana nowadays has a submediterranean distribution, occupying habitats that are slightly warmer, moister, and less seasonal in temperature but more seasonal in precipitation than E. seguieriana, a characteristic species of continental steppes. Using flow cytometry, we demonstrate that the relative genome sizes of E. niciciana and E. seguieriana differ significantly. Additionally, multivariate morphometric analyses of 56 morphological characters indicated clear morphological divergence of the two species. Importantly, we also provide a revised taxonomic treatment including formal nomenclatural changes, an identification key and species descriptions. Our study demonstrates that an integrative approach, combining modern phylogenomic methods with traditional phylogenetic, cytogenetic, environmental and morphological analyses can result in satisfactorily resolved relationships in intricate groups of closely related species. Finally, phylogenetic inference using ITS sequences is still a useful tool for resolving relationships among the taxa at the species level, but the phylogenomic approach based on RADseq data certainly provides better resolution both among and within species.Austrian Science Fund Tiroler Wissenschaftsfond

Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction

Three-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing programme and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. The role of RIF1 in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing programme and nuclear architecture

Mask formulas for cograssmannian Kazhdan-Lusztig polynomials

We give two contructions of sets of masks on cograssmannian permutations that can be used in Deodhar's formula for Kazhdan-Lusztig basis elements of the Iwahori-Hecke algebra. The constructions are respectively based on a formula of Lascoux-Schutzenberger and its geometric interpretation by Zelevinsky. The first construction relies on a basis of the Hecke algebra constructed from principal lower order ideals in Bruhat order and a translation of this basis into sets of masks. The second construction relies on an interpretation of masks as cells of the Bott-Samelson resolution. These constructions give distinct answers to a question of Deodhar.Comment: 43 page

Complete solutions to the metric of spherically collapsing dust in an expanding spacetime with a cosmological constant

We present semi-analytical solutions to the background equations describing the Lema\^itre-Tolman-Bondi (LTB) metric as well as the homogeneous Friedmann equations, in the presence of dust, curvature and a cosmological constant Lambda. For none of the presented solutions any numerical integration has to be performed. All presented solutions are given for expanding and collapsing phases, preserving continuity in time and radius. Hence, these solutions describe the complete space time of a collapsing spherical object in an expanding universe. In the appendix we present for completeness a solution of the Friedmann equations in the additional presence of radiation, only valid for the Robertson-Walker metric.Comment: 23 pages, one figure. Numerical module for evaluation of the solutions released at http://web.physik.rwth-aachen.de/download/valkenburg/ColLambda/ Matches published version, published under Open Access. Note change of titl

Patient-reported outcomes with durvalumab, with or without tremelimumab, plus chemotherapy as first-line treatment for metastatic non-small-cell lung cancer (POSEIDON).

In the phase 3 POSEIDON study, first-line tremelimumab plus durvalumab and chemotherapy significantly improved overall survival and progression-free survival versus chemotherapy in metastatic non-small-cell lung cancer (NSCLC). We present patient-reported outcomes (PROs). Treatment-naïve patients were randomized 1:1:1 to tremelimumab plus durvalumab and chemotherapy, durvalumab plus chemotherapy, or chemotherapy. PROs (prespecified secondary endpoints) were assessed using the European Organisation for Research and Treatment of Cancer 30-item core quality of life questionnaire version 3 (QLQ-C30) and its 13-item lung cancer module (QLQ-LC13). We analyzed time to deterioration (TTD) of symptoms, functioning, and global health status/quality of life (QoL) from randomization by log-rank test and improvement rates by logistic regression. 972/1013 (96 %) patients randomized completed baseline QLQ-C30 and QLQ-LC13 questionnaires, with scores comparable between treatment arms. Patients receiving tremelimumab plus durvalumab and chemotherapy versus chemotherapy had longer median TTD for all PRO items. Hazard ratios for TTD favored tremelimumab plus durvalumab and chemotherapy for all items except diarrhea; 95 % confidence intervals did not cross 1.0 for global health status/QoL, physical functioning, cognitive functioning, pain, nausea/vomiting, insomnia, constipation, hemoptysis, dyspnea, and pain in other parts. For durvalumab plus chemotherapy, median TTD was longer versus chemotherapy for all items except nausea/vomiting and diarrhea. Hazard ratios favored durvalumab plus chemotherapy for all items except appetite loss; 95 % confidence intervals did not cross 1.0 for global health status/QoL, physical functioning, role functioning, dyspnea, and pain in other parts. For both immunotherapy plus chemotherapy arms, improvement rates in all PRO items were numerically higher versus chemotherapy, with odds ratios > 1. Tremelimumab plus durvalumab and chemotherapy delayed deterioration in symptoms, functioning, and global health status/QoL compared with chemotherapy. Together with significant improvements in survival, these results support tremelimumab plus durvalumab and chemotherapy as a first-line treatment option in metastatic NSCLC

On the role of the magnetic dipolar interaction in cold and ultracold collisions: Numerical and analytical results for NH(3Σ−^3\Sigma^-) + NH(3Σ−^3\Sigma^-)

We present a detailed analysis of the role of the magnetic dipole-dipole interaction in cold and ultracold collisions. We focus on collisions between magnetically trapped NH molecules, but the theory is general for any two paramagnetic species for which the electronic spin and its space-fixed projection are (approximately) good quantum numbers. It is shown that dipolar spin relaxation is directly associated with magnetic-dipole induced avoided crossings that occur between different adiabatic potential curves. For a given collision energy and magnetic field strength, the cross-section contributions from different scattering channels depend strongly on whether or not the corresponding avoided crossings are energetically accessible. We find that the crossings become lower in energy as the magnetic field decreases, so that higher partial-wave scattering becomes increasingly important \textit{below} a certain magnetic field strength. In addition, we derive analytical cross-section expressions for dipolar spin relaxation based on the Born approximation and distorted-wave Born approximation. The validity regions of these analytical expressions are determined by comparison with the NH + NH cross sections obtained from full coupled-channel calculations. We find that the Born approximation is accurate over a wide range of energies and field strengths, but breaks down at high energies and high magnetic fields. The analytical distorted-wave Born approximation gives more accurate results in the case of s-wave scattering, but shows some significant discrepancies for the higher partial-wave channels. We thus conclude that the Born approximation gives generally more meaningful results than the distorted-wave Born approximation at the collision energies and fields considered in this work.Comment: Accepted by Eur. Phys. J. D for publication in Special Issue on Cold Quantum Matter - Achievements and Prospects (2011

Gravitational Lensing by Black Holes

We review the theoretical aspects of gravitational lensing by black holes, and discuss the perspectives for realistic observations. We will first treat lensing by spherically symmetric black holes, in which the formation of infinite sequences of higher order images emerges in the clearest way. We will then consider the effects of the spin of the black hole, with the formation of giant higher order caustics and multiple images. Finally, we will consider the perspectives for observations of black hole lensing, from the detection of secondary images of stellar sources and spots on the accretion disk to the interpretation of iron K-lines and direct imaging of the shadow of the black hole.Comment: Invited article for the GRG special issue on lensing (P. Jetzer, Y. Mellier and V. Perlick Eds.). 31 pages, 12 figure

Caustic Formation in Tachyon Effective Field Theories

Certain configurations of D-branes, for example wrong dimensional branes or the brane-antibrane system, are unstable to decay. This instability is described by the appearance of a tachyonic mode in the spectrum of open strings ending on the brane(s). The decay of these unstable systems is described by the rolling of the tachyon field from the unstable maximum to the minimum of its potential. We analytically study the dynamics of the inhomogeneous tachyon field as it rolls towards the true vacuum of the theory in the context of several different tachyon effective actions. We find that the vacuum dynamics of these theories is remarkably similar and in particular we show that in all cases the tachyon field forms caustics where second and higher derivatives of the field blow up. The formation of caustics signals a pathology in the evolution since each of the effective actions considered is not reliable in the vicinity of a caustic. We speculate that the formation of caustics is an artifact of truncating the tachyon action, which should contain all orders of derivatives acting on the field, to a finite number of derivatives. Finally, we consider inhomogeneous solutions in p-adic string theory, a toy model of the bosonic tachyon which contains derivatives of all orders acting on the field. For a large class of initial conditions we conclusively show that the evolution is well behaved in this case. It is unclear if these caustics are a genuine prediction of string theory or not.Comment: 23 pages, 5 figures; accepted for publication in JHEP. Revised derivation of eikonal equation for the DBI action. Added comments concerning the relationship between p-adic string theory and tachyon matter. Added second example of inhomogeneous evolution in p-adic string theory. Misleading statements concerning caustic-free evolution removed, references adde

Linear Collider Capabilities for Supersymmetry in Dark Matter Allowed Regions of the mSUGRA Model

Recent comparisons of minimal supergravity (mSUGRA) model predictions with WMAP measurements of the neutralino relic density point to preferred regions of model parameter space. We investigate the reach of linear colliders (LC) with $\sqrt{s}=0.5$ and 1 TeV for SUSY in the framework of the mSUGRA model. We find that LCs can cover the entire stau co-annihilation region provided \tan\beta \alt 30. In the hyperbolic branch/focus point (HB/FP) region of parameter space, specialized cuts are suggested to increase the reach in this important ``dark matter allowed'' area. In the case of the HB/FP region, the reach of a LC extends well past the reach of the CERN LHC. We examine a case study in the HB/FP region, and show that the MSSM parameters $\mu$ and $M_2$ can be sufficiently well-measured to demonstrate that one would indeed be in the HB/FP region, where the lightest chargino and neutralino have a substantial higgsino component.Comment: 29 pages, 15 EPS figures; updated version slightly modified to conform with published versio