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

Novel synovial fluid recovery method allows for quantification of a marker of arthritis in mice

SummaryObjectiveWe evaluated three methodologies – a calcium sodium alginate compound (CSAC), polyacrylate beads (PABs), and Whatman paper recovery (WPR) – for the ability to recover synovial fluid (SF) from mouse knees in a manner that facilitated biochemical marker analysis.MethodsPilot testing of each of these recovery vehicles was conducted using small volumes of waste human SF. CSAC emerged as the method of choice, and was used to recover and quantify SF from the knees of C57BL/6 mice (n=12), six of which were given left knee articular fractures. SF concentrations of cartilage oligomeric matrix protein (COMP) were measured by enzyme-linked immunosorbent assay.ResultsThe mean concentration ratio [(COMPleft knee)/(COMPright knee)] was higher in the mice subjected to articular fracture when compared to the non-fracture mice (P=0.026). The mean total COMP ratio (taking into account the quantitative recovery of SF) best discriminated between fracture and non-fracture knees (P=0.004).ConclusionsOur results provide the first direct evidence of accelerated joint tissue turnover in a mouse model responding to acute joint injury. These data strongly suggest that mouse SF recovery is feasible and that biomarker analysis of collected SF samples can augment traditional histological analyses in mouse models of arthritis

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

Seasonal size variation in the predatory cladoceran Bythotrephes cederstroemii in Lake Michigan

1.  Dry weight, body length and spine length were measured for the exotic cladoceran Bythotrephes cederstroemii collected from offshore and inshore stations in southeastern Lake Michigan. Average dry weight of each developmental stage exhibited seasonal variation by a factor of more than 5. 2.  Mean dry weight of Bythotrephes was closely correlated with water temperature. Contrary to the inverse relationship between water temperature and body size frequently observed for other invertebrates, the dry weight of Bythotrephes increased at higher ambient temperatures. 3.  No significant correlation was observed between abundances of major zooplankton taxa and the dry weight of Bythotrephes . An indirect effect of temperature on prey consumption may cause seasonal variation in dry weight of Bythotrephes in Lake Michigan. 4.  Distances between adjacent pairs of barbs, added to the caudal spine with each moult, are significantly shorter in Bythotrephes which produce resting eggs. Less material investment in the exoskeleton of sexually reproducing females was observed in favour of growth and reproduction.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74641/1/j.1365-2427.1994.tb00842.x.pd

Assessing sulfate reduction and methane cycling in a high salinity pore water system in the northern Gulf of Mexico

This paper is not subject to U.S. copyright. The definitive version was published in Marine and Petroleum Geology 25 (2008): 942-951, doi:10.1016/j.marpetgeo.2008.01.016.Pore waters extracted from 18 piston cores obtained on and near a salt-cored bathymetric high in Keathley Canyon lease block 151 in the northern Gulf of Mexico contain elevated concentrations of chloride (up to 838 mM) and have pore water chemical concentration profiles that exhibit extensive departures (concavity) from steady-state (linear) diffusive equilibrium with depth. Minimum δ13C dissolved inorganic carbon (DIC) values of −55.9‰ to −64.8‰ at the sulfate–methane transition (SMT) strongly suggest active anaerobic oxidation of methane (AOM) throughout the study region. However, the nonlinear pore water chemistry-depth profiles make it impossible to determine the vertical extent of active AOM or the potential role of alternate sulfate reduction pathways. Here we utilize the conservative (non-reactive) nature of dissolved chloride to differentiate the effects of biogeochemical activity (e.g., AOM and/or organoclastic sulfate reduction) relative to physical mixing in high salinity Keathley Canyon sediments. In most cases, the DIC and sulfate concentrations in pore waters are consistent with a conservative mixing model that uses chloride concentrations at the seafloor and the SMT as endmembers. Conservative mixing of pore water constituents implies that an undetermined physical process is primarily responsible for the nonlinearity of the pore water-depth profiles. In limited cases where the sulfate and DIC concentrations deviated from conservative mixing between the seafloor and SMT, the δ13C-DIC mixing diagrams suggest that the excess DIC is produced from a 13C-depleted source that could only be accounted for by microbial methane, the dominant form of methane identified during this study. We conclude that AOM is the most prevalent sink for sulfate and that it occurs primarily at the SMT at this Keathley Canyon site.This work was supported by DOE’s National Energy Technology Laboratory, the Office of Naval Research, and the Naval Research Laboratory. J.W.P was supported by a USGS Mendenhall Postdoctoral Research Fellowship Program during preparation of this manuscript

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

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 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