Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

L). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages

FLICK: Developing and running application-specific network services

Data centre networks are increasingly programmable, with $\textit{application-specific}$ network services proliferating, from custom load-balancers to middleboxes providing caching and aggregation. Developers must currently implement these services using traditional low-level APIs, which neither support natural operations on application data nor provide efficient performance isolation. We describe FLICK, a framework for the programming and execution of application-specific network services on multi-core CPUs. Developers write network services in the FLICK $\textit{language}$, which offers high-level processing constructs and application-relevant data types. FLICK programs are translated automatically to efficient, parallel $\textit{task graphs}$, implemented in C++ on top of a user-space TCP stack. Task graphs have bounded resource usage at runtime, which means that the graphs of multiple services can execute concurrently without interference using cooperative scheduling. We evaluate FLICK with several services (an HTTP load-balancer, a Memcached router and a Hadoop data aggregator), showing that it achieves good performance while reducing development effort.Engineering and Physical Sciences Research CouncilThis is the author accepted manuscript. The final version is available from USENIX via https://www.usenix.org/conference/atc16/technical-sessions/presentation/ali

Aspects of holography for theories with hyperscaling violation

We analyze various aspects of the recently proposed holographic theories with general dynamical critical exponent z and hyperscaling violation exponent $\theta$. We first find the basic constraints on $z, \theta$ from the gravity side, and compute the stress-energy tensor expectation values and scalar two-point functions. Massive correlators exhibit a nontrivial exponential behavior at long distances, controlled by $\theta$. At short distance, the two-point functions become power-law, with a universal form for $\theta > 0$. Next, the calculation of the holographic entanglement entropy reveals the existence of novel phases which violate the area law. The entropy in these phases has a behavior that interpolates between that of a Fermi surface and that exhibited by systems with extensive entanglement entropy. Finally, we describe microscopic embeddings of some $\theta \neq 0$ metrics into full string theory models -- these metrics characterize large regions of the parameter space of Dp-brane metrics for $p\neq 3$. For instance, the theory of N D2-branes in IIA supergravity has z=1 and $\theta = -1/3$ over a wide range of scales, at large $g_s N$.Comment: 35 pages; v2: new references added; v3: proper reference [14] added; v4: minor clarification

A review of elliptical and disc galaxy structure, and modern scaling laws

A century ago, in 1911 and 1913, Plummer and then Reynolds introduced their models to describe the radial distribution of stars in `nebulae'. This article reviews the progress since then, providing both an historical perspective and a contemporary review of the stellar structure of bulges, discs and elliptical galaxies. The quantification of galaxy nuclei, such as central mass deficits and excess nuclear light, plus the structure of dark matter halos and cD galaxy envelopes, are discussed. Issues pertaining to spiral galaxies including dust, bulge-to-disc ratios, bulgeless galaxies, bars and the identification of pseudobulges are also reviewed. An array of modern scaling relations involving sizes, luminosities, surface brightnesses and stellar concentrations are presented, many of which are shown to be curved. These 'redshift zero' relations not only quantify the behavior and nature of galaxies in the Universe today, but are the modern benchmark for evolutionary studies of galaxies, whether based on observations, N-body-simulations or semi-analytical modelling. For example, it is shown that some of the recently discovered compact elliptical galaxies at 1.5 < z < 2.5 may be the bulges of modern disc galaxies.Comment: Condensed version (due to Contract) of an invited review article to appear in "Planets, Stars and Stellar Systems"(www.springer.com/astronomy/book/978-90-481-8818-5). 500+ references incl. many somewhat forgotten, pioneer papers. Original submission to Springer: 07-June-201

A tumor cord model for Doxorubicin delivery and dose optimization in solid tumors

<p>Abstract</p> <p>Background</p> <p>Doxorubicin is a common anticancer agent used in the treatment of a number of neoplasms, with the lifetime dose limited due to the potential for cardiotoxocity. This has motivated efforts to develop optimal dosage regimes that maximize anti-tumor activity while minimizing cardiac toxicity, which is correlated with peak plasma concentration. Doxorubicin is characterized by poor penetration from tumoral vessels into the tumor mass, due to the highly irregular tumor vasculature. I model the delivery of a soluble drug from the vasculature to a solid tumor using a tumor cord model and examine the penetration of doxorubicin under different dosage regimes and tumor microenvironments.</p> <p>Methods</p> <p>A coupled ODE-PDE model is employed where drug is transported from the vasculature into a tumor cord domain according to the principle of solute transport. Within the tumor cord, extracellular drug diffuses and saturable pharmacokinetics govern uptake and efflux by cancer cells. Cancer cell death is also determined as a function of peak intracellular drug concentration.</p> <p>Results</p> <p>The model predicts that transport to the tumor cord from the vasculature is dominated by diffusive transport of free drug during the initial plasma drug distribution phase. I characterize the effect of all parameters describing the tumor microenvironment on drug delivery, and large intercapillary distance is predicted to be a major barrier to drug delivery. Comparing continuous drug infusion with bolus injection shows that the optimum infusion time depends upon the drug dose, with bolus injection best for low-dose therapy but short infusions better for high doses. Simulations of multiple treatments suggest that additional treatments have similar efficacy in terms of cell mortality, but drug penetration is limited. Moreover, fractionating a single large dose into several smaller doses slightly improves anti-tumor efficacy.</p> <p>Conclusion</p> <p>Drug infusion time has a significant effect on the spatial profile of cell mortality within tumor cord systems. Therefore, extending infusion times (up to 2 hours) and fractionating large doses are two strategies that may preserve or increase anti-tumor activity and reduce cardiotoxicity by decreasing peak plasma concentration. However, even under optimal conditions, doxorubicin may have limited delivery into advanced solid tumors.</p

Reconstructing the three-dimensional GABAergic microcircuit of the striatum

A system's wiring constrains its dynamics, yet modelling of neural structures often overlooks the specific networks formed by their neurons. We developed an approach for constructing anatomically realistic networks and reconstructed the GABAergic microcircuit formed by the medium spiny neurons (MSNs) and fast-spiking interneurons (FSIs) of the adult rat striatum. We grew dendrite and axon models for these neurons and extracted probabilities for the presence of these neurites as a function of distance from the soma. From these, we found the probabilities of intersection between the neurites of two neurons given their inter-somatic distance, and used these to construct three-dimensional striatal networks. The MSN dendrite models predicted that half of all dendritic spines are within 100 mu m of the soma. The constructed networks predict distributions of gap junctions between FSI dendrites, synaptic contacts between MSNs, and synaptic inputs from FSIs to MSNs that are consistent with current estimates. The models predict that to achieve this, FSIs should be at most 1% of the striatal population. They also show that the striatum is sparsely connected: FSI-MSN and MSN-MSN contacts respectively form 7% and 1.7% of all possible connections. The models predict two striking network properties: the dominant GABAergic input to a MSN arises from neurons with somas at the edge of its dendritic field; and FSIs are interconnected on two different spatial scales: locally by gap junctions and distally by synapses. We show that both properties influence striatal dynamics: the most potent inhibition of a MSN arises from a region of striatum at the edge of its dendritic field; and the combination of local gap junction and distal synaptic networks between FSIs sets a robust input-output regime for the MSN population. Our models thus intimately link striatal micro-anatomy to its dynamics, providing a biologically grounded platform for further study

A remarkable recurrent nova in M31: Discovery and optical/UV observations of the predicted 2014 eruption

The Andromeda Galaxy recurrent nova M31N 2008-12a had been caught in eruption eight times. The inter-eruption period of M31N 2008-12a is ~1 year, making it the most rapidly recurring system known, and a strong single-degenerate Type Ia Supernova progenitor candidate. Following the 2013 eruption, a campaign was initiated to detect the predicted 2014 eruption and to then perform high cadence optical photometric and spectroscopic monitoring using ground-based telescopes, along with rapid UV and X-ray follow-up with the Swift satellite. Here we report the results of a high cadence multicolour optical monitoring campaign, the spectroscopic evolution, and the UV photometry. We also discuss tantalising evidence of a potentially related, vastly-extended, nebulosity. The 2014 eruption was discovered, before optical maximum, on October 2, 2014. We find that the optical properties of M31N 2008-12a evolve faster than all Galactic recurrent novae known, and all its eruptions show remarkable similarity both photometrically and spectroscopically. Optical spectra were obtained as early as 0.26 days post maximum, and again confirm the nova nature of the eruption. A significant deceleration of the inferred ejecta expansion velocity is observed which may be caused by interaction of the ejecta with surrounding material, possibly a red giant wind. We find a low ejected mass and low ejection velocity, which are consistent with high mass-accretion rate, high mass white dwarf, and short recurrence time models of novae. We encourage additional observations, especially around the predicted time of the next eruption, towards the end of 2015

Circumstellar disks and planets. Science cases for next-generation optical/infrared long-baseline interferometers

We present a review of the interplay between the evolution of circumstellar disks and the formation of planets, both from the perspective of theoretical models and dedicated observations. Based on this, we identify and discuss fundamental questions concerning the formation and evolution of circumstellar disks and planets which can be addressed in the near future with optical and infrared long-baseline interferometers. Furthermore, the importance of complementary observations with long-baseline (sub)millimeter interferometers and high-sensitivity infrared observatories is outlined.Comment: 83 pages; Accepted for publication in "Astronomy and Astrophysics Review"; The final publication is available at http://www.springerlink.co