A comparison of benthic macroinvertebrate assemblages among kryal and rhithral lake outlets in the North Cascade Mountains

This study compares the physico-chemical conditions and composition of benthic macroinvertebrates from five rhithral (snowmelt-fed) and five kryal (glacially-fed) lake outlet streams in the North Cascade Mountains, WA. Non-metric, non-parametric cluster and association analysis (NMCAA) clearly separated outlet streams of kryal and rhithral origin based on physico-chemical and taxon variables. Kryal lake outlets were characterized by lower water temperatures, unstable in-stream channels and higher turbidity, discharge and fine substrates than rhithral sites. A total of 24,985 specimens representing 93 macroinvertebrate taxa were collected. Rhithral lake outlets had significantly higher densities and supported more taxa than kryal sites (9,049 ind./m2 and 77 taxa versus 821 ind./m2 and 35 taxa). Chironomidae were the dominant taxon amongst all sites, although densities and taxa richness were one-third in the kryal lake outlets when compared to rhithral sites. Rhithral lake outlets contained higher densities of non-insect taxa such as Acari, Oligochaeta, Nemathelminthes, Planariidae and crustaceans. Water temperature, stream discharge and turbidity were the variables most strongly correlated to density and taxa richness. My results suggest that glacial presence was the dominant factor influencing instream environmental conditions and subsequently macroinvertebrate assemblages of alpine lake outlet streams

Parallelization and optimization of genetic analyses in isolation by distance web service

<p>Abstract</p> <p>Background</p> <p>The Isolation by Distance Web Service (IBDWS) is a user-friendly web interface for analyzing patterns of isolation by distance in population genetic data. IBDWS enables researchers to perform a variety of statistical tests such as Mantel tests and reduced major axis regression (RMA), and returns vector based graphs. The more than 60 citations since 2005 confirm the popularity and utility of this website. Despite its usefulness, the data sets with over 65 populations can take hours or days to complete due to the computational intensity of the statistical tests. This is especially troublesome for web-based software analysis, since users tend to expect real-time results on the order of seconds, or at most, minutes. Moreover, as genetic data continue to increase and diversify, so does the demand for more processing power. In order to increase the speed and efficiency of IBDWS, we first determined which aspects of the code were most time consuming and whether they might be amenable to improvements by parallelization or algorithmic optimization.</p> <p>Results</p> <p>Runtime tests uncovered two areas of IBDWS that consumed significant amounts of time: randomizations within the Mantel test and the RMA calculations. We found that these sections of code could be restructured and parallelized to improve efficiency. The code was first optimized by combining two similar randomization routines, implementing a Fisher-Yates shuffling algorithm, and then parallelizing those routines. Tests of the parallelization and Fisher-Yates algorithmic improvements were performed on a variety of data sets ranging from 10 to 150 populations. All tested algorithms showed runtime reductions and a very close fit to the predicted speedups based on time-complexity calculations. In the case of 150 populations with 10,000 randomizations, data were analyzed 23 times faster.</p> <p>Conclusion</p> <p>Since the implementation of the new algorithms in late 2007, datasets have continued to increase substantially in size and many exceed the largest population sizes we used in our test sets. The fact that the website has continued to work well in "real-world" tests, and receives a considerable number of new citations provides the strongest testimony to the effectiveness of our improvements. However, we soon expect the need to upgrade the number of nodes in our cluster significantly as dataset sizes continue to expand. The parallel implementation can be found at <url>http://ibdws.sdsu.edu/</url>.</p

The quest to model chronic traumatic encephalopathy: a multiple model and injury paradigm experience

Chronic neurodegeneration following a history of neurotrauma is frequently associated with neuropsychiatric and cognitive symptoms. In order to enhance understanding about the underlying pathophysiology linking neurotrauma to neurodegeneration, a multi-model preclinical approach must be established to account for the different injury paradigms and pathophysiologic mechanisms. We investigated the development of tau pathology and behavioral changes using a multi-model and multi-institutional approach, comparing the preclinical results to tauopathy patterns seen in post-mortem human samples from athletes diagnosed with chronic traumatic encephalopathy (CTE). We utilized a scaled and validated blast-induced traumatic brain injury model in rats and a modified pneumatic closed-head impact model in mice. Tau hyperphosphorylation was evaluated by western blot and immunohistochemistry. Elevated-plus maze and Morris water maze were employed to measure impulsive-like behavior and cognitive deficits respectively. Animals exposed to single blast (~50 PSI reflected peak overpressure) exhibited elevated AT8 immunoreactivity in the contralateral hippocampus at 1 month compared to controls (q = 3.96, p \u3c 0.05). Animals exposed to repeat blast (six blasts over 2 weeks) had increased AT8 (q = 8.12, p \u3c 0.001) and AT270 (q = 4.03, p \u3c 0.05) in the contralateral hippocampus at 1 month post-injury compared to controls. In the modified controlled closed-head impact mouse model, no significant difference in AT8 was seen at 7 days, however a significant elevation was detected at 1 month following injury in the ipsilateral hippocampus compared to control (q = 4.34, p \u3c 0.05). Elevated-plus maze data revealed that rats exposed to single blast (q = 3.53, p \u3c 0.05) and repeat blast (q = 4.21, p \u3c 0.05) spent more time in seconds exploring the open arms compared to controls. Morris water maze testing revealed a significant difference between groups in acquisition times on days 22–27. During the probe trial, single blast (t = 6.44, p \u3c 0.05) and repeat blast (t = 8.00, p \u3c 0.05) rats spent less time in seconds exploring where the platform had been located compared to controls. This study provides a multi-model example of replicating tau and behavioral changes in animals and provides a foundation for future investigation of CTE disease pathophysiology and therapeutic development

The Be/X-ray transient KS 1947+300

We present optical spectroscopy and optical and infrared photometry of the counterpart to the transient X-ray source KS 1947+300. The counterpart is shown to be a moderately reddened V=14.2 early-type Be star located in an area of low interstellar absorption slightly above the Galactic plane. Changes in brightness are accompanied by correlated reddening of the source, as is expected in this kind of object. From intermediate resolution spectroscopy, we derive a spectral type B0Ve. If the intrinsic luminosity of the star is normal for its spectral type, KS 1947+300 is situated at a distance of ~10 kpc, implying that its X-ray luminosity at the peak of the spring 2000 X-ray outburst was typical of Type II outbursts in Be/X-ray transients. KS 1947+300 is thus the first Be/X-ray recurrent transient showing Type II outbursts which has an almost circular orbit.Comment: 7 pages, 5 figures, uses new A&A format (included). Accepted for publication in A&

Ice-Tethered Profiler observations of the double-diffusive staircase in the Canada Basin thermocline

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C00A02, doi:10.1029/2008JC004829.Six Ice-Tethered Profilers (ITP), deployed in the central Canada Basin of the Arctic Ocean between 2004 and 2007, have provided detailed potential temperature and salinity measurements of a double-diffusive staircase at about 200–300 m depth. Individual layers in the staircase are of order 1 m in vertical height but appear to extend horizontally for hundreds of kilometers, with along-layer gradients of temperature and salinity tightly related. On the basis of laboratory-derived double-diffusive flux laws, estimated vertical heat fluxes through the staircase are in the range 0.05–0.3 W m−2, only about one tenth of the estimated mean surface mixed layer heat flux to the sea ice. It is thus concluded that the vertical transport of heat from the Atlantic Water in the central basin is unlikely to have a significant impact to the Canada Basin ocean surface heat budget. Icebreaker conductivity-temperature-depth data from the Beaufort Gyre Freshwater Experiment show that the staircase is absent at the basin periphery. Turbulent mixing that presumably disrupts the staircase might drive greater flux from the Atlantic Water at the basin boundaries and possibly dominate the regionally averaged heat flux.Funding for construction and deployment of the prototype ITPs was provided by the National Science Foundation Oceanographic Technology and Interdisciplinary Coordination (OTIC) Program and Office of Polar Programs (OPP) under grant OCE-0324233. Continued support for the ITP field program and data analysis has been provided by the OPP Arctic Sciences Section under awards ARC-0519899, ARC-0631951, ARC-0713837, and internal WHOI funding

A model for transition of 5 '-nuclease domain of DNA polymerase I from inert to active modes

Bacteria contain DNA polymerase I (PolI), a single polypeptide chain consisting of similar to 930 residues, possessing DNA-dependent DNA polymerase, 3'-5' proofreading and 5'-3' exonuclease (also known as flap endonuclease) activities. PolI is particularly important in the processing of Okazaki fragments generated during lagging strand replication and must ultimately produce a double-stranded substrate with a nick suitable for DNA ligase to seal. PolI's activities must be highly coordinated both temporally and spatially otherwise uncontrolled 5'-nuclease activity could attack a nick and produce extended gaps leading to potentially lethal double-strand breaks. To investigate the mechanism of how PolI efficiently produces these nicks, we present theoretical studies on the dynamics of two possible scenarios or models. In one the flap DNA substrate can transit from the polymerase active site to the 5'-nuclease active site, with the relative position of the two active sites being kept fixed; while the other is that the 5'-nuclease domain can transit from the inactive mode, with the 5'-nuclease active site distant from the cleavage site on the DNA substrate, to the active mode, where the active site and substrate cleavage site are juxtaposed. The theoretical results based on the former scenario are inconsistent with the available experimental data that indicated that the majority of 5'-nucleolytic processing events are carried out by the same PolI molecule that has just extended the upstream primer terminus. By contrast, the theoretical results on the latter model, which is constructed based on available structural studies, are consistent with the experimental data. We thus conclude that the latter model rather than the former one is reasonable to describe the cooperation of the PolI's polymerase and 5'-3' exonuclease activities. Moreover, predicted results for the latter model are presented

Balancing the dilution and oddity effects: Decisions depend on body size

Background Grouping behaviour, common across the animal kingdom, is known to reduce an individual's risk of predation; particularly through dilution of individual risk and predator confusion (predator inability to single out an individual for attack). Theory predicts greater risk of predation to individuals more conspicuous to predators by difference in appearance from the group (the ‘oddity’ effect). Thus, animals should choose group mates close in appearance to themselves (eg. similar size), whilst also choosing a large group. Methodology and Principal Findings We used the Trinidadian guppy (Poecilia reticulata), a well known model species of group-living freshwater fish, in a series of binary choice trials investigating the outcome of conflict between preferences for large and phenotypically matched groups along a predation risk gradient. We found body-size dependent differences in the resultant social decisions. Large fish preferred shoaling with size-matched individuals, while small fish demonstrated no preference. There was a trend towards reduced preferences for the matched shoal under increased predation risk. Small fish were more active than large fish, moving between shoals more frequently. Activity levels increased as predation risk decreased. We found no effect of unmatched shoal size on preferences or activity. Conclusions and Significance Our results suggest that predation risk and individual body size act together to influence shoaling decisions. Oddity was more important for large than small fish, reducing in importance at higher predation risks. Dilution was potentially of limited importance at these shoal sizes. Activity levels may relate to how much sampling of each shoal was needed by the test fish during decision making. Predation pressure may select for better decision makers to survive to larger size, or that older, larger fish have learned to make shoaling decisions more efficiently, and this, combined with their size relative to shoal-mates, and attractiveness as prey items influences shoaling decisions

The NANOGrav 11-Year Data Set: Limits on Gravitational Waves from Individual Supermassive Black Hole Binaries

Observations indicate that nearly all galaxies contain supermassive black holes (SMBHs) at their centers. When galaxies merge, their component black holes form SMBH binaries (SMBHBs), which emit low-frequency gravitational waves (GWs) that can be detected by pulsar timing arrays (PTAs). We have searched the recently-released North American Nanohertz Observatory for Gravitational Waves (NANOGrav) 11-year data set for GWs from individual SMBHBs in circular orbits. As we did not find strong evidence for GWs in our data, we placed 95\% upper limits on the strength of GWs from such sources as a function of GW frequency and sky location. We placed a sky-averaged upper limit on the GW strain of $h_0 < 7.3(3) \times 10^{-15}$ at $f_\mathrm{gw}= 8$ nHz. We also developed a technique to determine the significance of a particular signal in each pulsar using ``dropout' parameters as a way of identifying spurious signals in measurements from individual pulsars. We used our upper limits on the GW strain to place lower limits on the distances to individual SMBHBs. At the most-sensitive sky location, we ruled out SMBHBs emitting GWs with $f_\mathrm{gw}= 8$ nHz within 120 Mpc for $\mathcal{M} = 10^9 \, M_\odot$, and within 5.5 Gpc for $\mathcal{M} = 10^{10} \, M_\odot$. We also determined that there are no SMBHBs with $\mathcal{M} > 1.6 \times 10^9 \, M_\odot$ emitting GWs in the Virgo Cluster. Finally, we estimated the number of potentially detectable sources given our current strain upper limits based on galaxies in Two Micron All-Sky Survey (2MASS) and merger rates from the Illustris cosmological simulation project. Only 34 out of 75,000 realizations of the local Universe contained a detectable source, from which we concluded it was unsurprising that we did not detect any individual sources given our current sensitivity to GWs.Comment: 10 pages, 11 figures. Accepted by Astrophysical Journal. Please send any comments/questions to S. J. Vigeland ([email protected]

Smoothed Particle Hydrodynamics (SPH) modelling of transient heat transfer in pulsed laser ablation of Al and associated free-surface problems

A Smoothed Particle Hydrodynamics (SPH) numerical model is developed to simulate pulsed-laser ablation processes for micro-machining. Heat diffusion behaviour of a specimen under the action of nanosecond pulsed lasers can be described analytically by using complementary error function solutions of second-order differential equations. However, their application is limited to cases without loss of material at the surface. Compared to conventional mesh-based techniques, as a novel meshless simulation method, SPH is ideally suited to applications with highly non-linear and explosive behaviour in laser ablation. However, little is known about the suitability of using SPH for the modelling of laser-material interactions with multiple phases at the micro scale. The present work investigates SPH modelling of pulsed-laser ablation of aluminium where the laser is applied directly to the free-surface boundary of the specimen. Having first assessed the performance of standard SPH surface treatments for functions commonly used to describe laser heating, the heat conduction behaviour of a new SPH methodology is then evaluated through a number of test cases for single- and multiple-pulse laser heating of aluminium showing excellent agreement when compared with an analytical solution. Simulation of real ablation processes, however, requires the model to capture the removal of material from the surface and its subsequent effects on the laser heating process. Hence, the SPH model for describing the transient behaviour of nanosecond laser ablation is validated with a number of experimental and reference results reported in the literature. The SPH model successfully predicts the material ablation depth profiles over a wide range of laser fluences 4–23 J/cm2 and pulse durations 6–10 ns, and also predicts the transient behaviour of the ejected material during the laser ablation process. Unlike conventional mesh-based methods, the SPH model was not only able to provide the thermo-physical properties of the ejected particles, but also the effect of the interaction between them as well as the direction and the pattern of the ejection