Assumption 0 analysis: comparative phylogenetic studies in the age of complexity

Darwin's panoramic view of biology encompassed two metaphors: the phylogenetic tree, pointing to relatively linear (and divergent) complexity, and the tangled bank, pointing to reticulated (and convergent) complexity. The emergence of phylogenetic systematics half a century ago made it possible to investigate linear complexity in biology. Assumption 0, first proposed in 1986, is not needed for cases of simple evolutionary patterns, but must be invoked when there are complex evolutionary patterns whose hallmark is reticulated relationships. A corollary of Assumption 0, the duplication convention, was proposed in 1990, permitting standard phylogenetic systematic ontology to be used in discovering reticulated evolutionary histories. In 2004, a new algorithm, phylogenetic analysis for comparing trees (PACT), was developed specifically for use in analyses invoking Assumption 0. PACT can help discern complex evolutionary explanations for historical biogeographical, coevolutionary, phylogenetic, and tokogenetic processe

PHYLO-ASP: Phylogenetic Systematics with Answer Set Programming

This note summarizes the use of Answer Set Programming to solve various computational problems to infer phylogenetic trees and phylogenetic networks, and discusses its applicability and effectiveness on some real taxa

Phylogeny of Geomydoecus and Thomomydoecus pocket gopher lice (phthiraptera, trichodectidae) inferred from cladistic analysis of adult and first instar morphology

The phylogeny for all 122 species and subspecies of chewing lice of the genera Geomydoecus and Thomomydoecus (Phthiraptera: Trichodectidae) hosted by pocket gophers (Rodentia: Geomyidae) is estimated by a cladistic analysis of fifty-eight morphological characters obtained from adults and first instars. The data set has considerable homoplasy, but still contains phylogenetic information. The phylogeny obtained is moderately resolved and, with some notable exceptions, supports the species complexes proposed by Hellenthal and Price over the the last two decades. The subgenera G. (Thaelerius) and T. (Thomomydoecus) are both shown to be monophyletic, but the monophly of subgenus T. (Jamespattonius) could not be confirmed, perhaps due to the lack of first-instar data for one of its component species. The nominate subgenus of Geomydoecus may be monophyletic, but our cladogram was insufficiently resolved to corroborate this. Mapping the pocket gopher hosts onto the phylogeny reveals a consistent pattern of louse clades being restricted to particular genera or subgenera of gophers, but the history of the host-parasite association appears complex and will require considerable effort to resolve

A Single-Lumen Central Venous Catheter for Continuous and Direct Intra-abdominal Pressure Measurement

Background: Abdominal compartment syndrome (ACS) is associated with high morbidity and mortality rates. Therefore, the need for a good diagnostic tool to predict intra-abdominal hypertension (IAH) and progression to ACS is paramount. Bladder pressure (BP) has been used for several years for intra-abdominal pressure (IAP) measurement but has the disadvantage that it is not a continuous measurement. In this study, a single-lumen central venous catheter (CVC) is placed through the abdominal wall into the abdominal cavity to continuously and directly monitor the intra-abdominal pressure (CDIAP). The aim of this study was to evaluate the use of CDIAP to measure BP as a representative of the true IAP. Methods: Both BP and CDIAP were prospectively recorded on a variety of surgical patients admitted to the intensive care unit (ICU) from March 2003 up to December 2004. At the end of the surgical procedure, the CVC was placed through the abdominal wall and connected to a pressure transducer. In addition, the BP was measured through the urine drainage port after clamping the catheter and filling the bladder with 50 ml of 0.9% saline. At least three paired measurements (BP and CDIAP) were performed for at least one day on the ICU in a standardized manner at preset time intervals on each patient. The paired measurements were compared using the Bland-Altman (B-A) method. Data are presented as mean ± standard deviation. Results: Over a period of 22 months (March 2003 until December 2004), 125 paired measurements of both BP and CDIAP were recorded on 25 patients. The mean age was 72.4 ± 6.6 years. Eighteen patients underwent central vascular surgery, and seven patients with peritonitis received laparotomy. The mean CDIAP was 11.4 ± 4.8 (range 2-30) mmHg, and the BP was 12.9 ± 5.3 (range 3-37) mmHg. The mean difference between CDIAP and BP was 1.6 ± 2.7 mmHg. There was an acceptable level of agreement (intraclass correlation 0.82) between IAP measured by BP and IAP measured via CDIAP. Conclusion: Continuous direct intra-abdominal pressure measurement proved that the BP measurement approach of Kron is representative of the IAP. CDIAP measurement is accurate and makes it easier for the nursing staff to be informed of the IAP

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

Measurement of D*+/- meson production in jets from pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

This paper reports a measurement of D*+/- meson production in jets from proton-proton collisions at a center-of-mass energy of sqrt(s) = 7 TeV at the CERN Large Hadron Collider. The measurement is based on a data sample recorded with the ATLAS detector with an integrated luminosity of 0.30 pb^-1 for jets with transverse momentum between 25 and 70 GeV in the pseudorapidity range |eta| < 2.5. D*+/- mesons found in jets are fully reconstructed in the decay chain: D*+ -> D0pi+, D0 -> K-pi+, and its charge conjugate. The production rate is found to be N(D*+/-)/N(jet) = 0.025 +/- 0.001(stat.) +/- 0.004(syst.) for D*+/- mesons that carry a fraction z of the jet momentum in the range 0.3 < z < 1. Monte Carlo predictions fail to describe the data at small values of z, and this is most marked at low jet transverse momentum.Comment: 10 pages plus author list (22 pages total), 5 figures, 1 table, matches published version in Physical Review

Layered control architectures in robots and vertebrates

We revieiv recent research in robotics, neuroscience, evolutionary neurobiology, and ethology with the aim of highlighting some points of agreement and convergence. Specifically, we com pare Brooks' (1986) subsumption architecture for robot control with research in neuroscience demonstrating layered control systems in vertebrate brains, and with research in ethology that emphasizes the decomposition of control into multiple, intertwined behavior systems. From this perspective we then describe interesting parallels between the subsumption architecture and the natural layered behavior system that determines defense reactions in the rat. We then consider the action selection problem for robots and vertebrates and argue that, in addition to subsumption- like conflict resolution mechanisms, the vertebrate nervous system employs specialized selection mechanisms located in a group of central brain structures termed the basal ganglia. We suggest that similar specialized switching mechanisms might be employed in layered robot control archi tectures to provide effective and flexible action selection

Search for supersymmetry in final states with jets, missing transverse momentum and one isolated lepton in sqrt{s} = 7 TeV pp collisions using 1 fb-1 of ATLAS data

We present an update of a search for supersymmetry in final states containing jets, missing transverse momentum, and one isolated electron or muon, using 1.04 fb^-1 of proton-proton collision data at sqrt{s} = 7 TeV recorded by the ATLAS experiment at the LHC in the first half of 2011. The analysis is carried out in four distinct signal regions with either three or four jets and variations on the (missing) transverse momentum cuts, resulting in optimized limits for various supersymmetry models. No excess above the standard model background expectation is observed. Limits are set on the visible cross-section of new physics within the kinematic requirements of the search. The results are interpreted as limits on the parameters of the minimal supergravity framework, limits on cross-sections of simplified models with specific squark and gluino decay modes, and limits on parameters of a model with bilinear R-parity violation.Comment: 18 pages plus author list (30 pages total), 9 figures, 4 tables, final version to appear in Physical Review

Reducing heterotic M-theory to five dimensional supergravity on a manifold with boundary

This paper constructs the reduction of heterotic $M$-theory in eleven dimensions to a supergravity model on a manifold with boundary in five dimensions using a Calabi-Yau three-fold. New results are presented for the boundary terms in the action and for the boundary conditions on the bulk fields. Some general features of dualisation on a manifold with boundary are used to explain the origin of some topological terms in the action. The effect of gaugino condensation on the fermion boundary conditions leads to a `twist' in the chirality of the gravitino which can provide an uplifting mechanism in the vacuum energy to cancel the cosmological constant after moduli stabilisation.Comment: 16 pages, RevTe