Escape path complexity and its context dependency in Pacific blue-eyes (Pseudomugil signifer)

The escape trajectories animals take following a predatory attack appear to show high degrees of apparent 'randomness' - a property that has been described as 'protean behaviour'. Here we present a method of quantifying the escape trajectories of individual animals using a path complexity approach. When fish (Pseudomugil signifer) were attacked either on their own or in groups, we find that an individual's path rapidly increases in entropy (our measure of complexity) following the attack. For individuals on their own, this entropy remains elevated (indicating a more random path) for a sustained period (10 seconds) after the attack, whilst it falls more quickly for individuals in groups. The entropy of the path is context dependent. When attacks towards single fish come from greater distances, a fish's path shows less complexity compared to attacks that come from short range. This context dependency effect did not exist, however, when individuals were in groups. Nor did the path complexity of individuals in groups depend on a fish's local density of neighbours. We separate out the components of speed and direction changes to determine which of these components contributes to the overall increase in path complexity following an attack. We found that both speed and direction measures contribute similarly to an individual's path's complexity in absolute terms. Our work highlights the adaptive behavioural tactics that animals use to avoid predators and also provides a novel method for quantifying the escape trajectories of animals.Comment: 9 page

On Beginning the Second Half Century

Observations on the 50th year of the Washington Law Review\u27s publication

CompGO: an R package for comparing and visualizing gene ontology enrichment differences between DNA binding experiments

Background: Gene ontology (GO) enrichment is commonly used for inferring biological meaning from systems biology experiments. However, determining differential GO and pathway enrichment between DNA-binding experiments or using the GO structure to classify experiments has received little attention. Results: Herein, we present a bioinformatics tool, CompGO, for identifying Differentially Enriched Gene Ontologies, called DiEGOs, and pathways, through the use of a z-score derivation of log odds ratios, and visualizing these differences at GO and pathway level. Through public experimental data focused on the cardiac transcription factor NKX2-5, we illustrate the problems associated with comparing GO enrichments between experiments using a simple overlap approach. Conclusions: We have developed an R/Bioconductor package, CompGO, which implements a new statistic normally used in epidemiological studies for performing comparative GO analyses and visualizing comparisons from .BED data containing genomic coordinates as well as gene lists as inputs. We justify the statistic through inclusion of experimental data and compare to the commonly used overlap method. CompGO is freely available as a R/Bioconductor package enabling easy integration into existing pipelines and is available at: http://www.bioconductor.org/packages/release/bioc/html/CompGO.html packages/release/bioc/html/CompGO.htm

Stable Water Isotopes Reveal Effects of Intermediate Disturbance and Canopy Structure on Forest Water Cycling

Forests play an integral role in the terrestrial water cycle and link exchanges of water between the land surface and the atmosphere. To examine the effects of an intermediate disturbance on forest water cycling, we compared vertical profiles of stable water vapor isotopes in two closely located forest sites in northern lower Michigan. At one site, all canopy‐dominant early successional species were stem girdled to induce mortality and accelerate senescence. At both sites, we measured the isotopic composition of atmospheric water vapor at six heights during three seasons (spring, summer, and fall) and paired vertical isotope profiles with local meteorology and sap flux. Disturbance had a substantial impact on local water cycling. The undisturbed canopy was moister, retained more transpired vapor, and at times was poorly mixed with the free atmosphere above the canopy. Differences between the disturbed and undisturbed sites were most pronounced in the summer when transpiration was high. Differences in forest structure at the two sites also led to more isotopically stratified vapor within the undisturbed canopy. Our findings suggest that intermediate disturbance may increase mixing between the surface layer and above‐canopy atmosphere and alter ecosystem‐atmosphere gas exchange.Plain Language SummaryForests play an important role in the climate system and link water fluxes between the land surface and the atmosphere. Here we compare water vapor isotopes in two adjacent forest sites in the northern lower peninsula of Michigan to understand the effects of intermediate disturbance and canopy structure on forest water cycling. One site is dominated by aspen and birch and has a thick, closed canopy. All of the aspen and birch were killed at the second site. As a result, the disturbed site has a more open‐canopy structure. From our comparison, we found that both the species of tree and the spacing around trees are important controls on forest water cycling. With more space between trees, air mixes more freely into the canopy, which dries the forest air. Alternatively, air may be poorly mixed within and above thick, closed canopies.Key PointsIntermediate disturbance can change the contribution of entrained, evaporated, and transpired water vapor to forest canopiesCanopy gaps increase hydrologic mixing between the surface layer and the free atmosphereThe assumption of a well‐mixed canopy atmosphere may be violated in the case of thick, homogeneous forest canopiesPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152563/1/jgrg21482_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152563/2/jgrg21482.pd

Comparative study of the commonly used virulence tests for laboratory diagnosis of ovine footrot caused by Dichelobacter nodosus in Australia.

Footrot in sheep and goats is expressed as a spectrum of clinical entities ranging from benign, which is a self limiting interdigital dermatitis to highly virulent, in which severe under running of the horn of the hoof occurs. Interactions between the host, the virulence of the causative strain of Dichelobacter nodosus and environmental conditions determine the severity of the disease. Clinical diagnosis of virulent footrot, which a notifiable disease in some states of Australia, is not always straightforward. Therefore, the Gelatin Gel and Elastase tests for protease activity, and the intA PCR test for an inserted genetic element in D. nodosus are commonly used to support or to confirm a clinical diagnosis. A comparative study of these laboratory tests with a large number of samples collected from 12 flocks of sheep with clinically virulent footrot was conducted. Based on the elastase test, 64% of the isolates tested were classified as virulent compared to 91% on the gelatin gel test and 41% according to the intA test. The agreement between the elastase and the gelatin gel test was low (kappa =0.12) as were the agreements between other tests. Only about 21% of the isolates were virulent in all 3 tests. Therefore these tests on their own may not provide standard and reliable results and are likely to remain as supplementary tests for clinical diagnosis of the disease. Keywords: Footrot, virulence, elastase test, gelatin gel test, intA PCR test

Sloan Digital Sky Survey III Photometric Quasar Clustering: Probing the Initial Conditions of the Universe using the Largest Volume

The Sloan Digital Sky Survey has surveyed 14,555 square degrees of the sky, and delivered over a trillion pixels of imaging data. We present the large-scale clustering of 1.6 million quasars between z = 0.5 and z = 2.5 that have been classified from this imaging, representing the highest density of quasars ever studied for clustering measurements. This data set spans ~11,000 square degrees and probes a volume of 80(Gpc/h)^3. In principle, such a large volume and medium density of tracers should facilitate high-precision cosmological constraints. We measure the angular clustering of photometrically classified quasars using an optimal quadratic estimator in four redshift slices with an accuracy of ~25% over a bin width of l ~10 - 15 on scales corresponding to matter-radiation equality and larger (l ~ 2 - 30). Observational systematics can strongly bias clustering measurements on large scales, which can mimic cosmologically relevant signals such as deviations from Gaussianity in the spectrum of primordial perturbations. We account for systematics by employing a new method recently proposed by Agarwal et al. (2014) to the clustering of photometrically classified quasars. We carefully apply our methodology to mitigate known observational systematics and further remove angular bins that are contaminated by unknown systematics. Combining quasar data with the photometric luminous red galaxy (LRG) sample of Ross et al. (2011) and Ho et al. (2012), and marginalizing over all bias and shot noise-like parameters, we obtain a constraint on local primordial non-Gaussianity of fNL = -113+/-154 (1\sigma error). [Abridged]Comment: 35 pages, 15 figure

Far-IR Measurements at Cerro Toco, Chile: FIRST, REFIR, and AERI

In mid-2009, the Radiative Heating in the Underexplored Bands Campaign II (RHUBC-II) was conducted from Cerro Toco, Chile, a high, dry, remote mountain plateau, 23degS , 67.8degW at 5.4km, in the Atacama Desert of Northern Chile. From this site, dominant IR water vapor absorption bands and continuum, saturated when viewed from the surface at lower altitudes, or in less dry locales, were investigated in detail, elucidating IR absorption and emission in the atmosphere. Three FTIR instruments were at the site, the Far-Infrared Spectroscopy of the Troposphere (FIRST), the Radiation Explorer in the Far Infrared (REFIR), and the Atmospheric Emitted Radiance Interferometer (AERI). In a side-by-side comparison, these measured atmospheric downwelling radiation, with overlapping spectral coverage from 5 to100um (2000 to 100/cm), and instrument spectral resolutions from 0.5 to 0.64/cm, unapodized. In addition to the FTIR and other ground-based IR and microwave instrumentation, pressure/temperature/relative humidity measuring sondes, for atmospheric profiles to 18km, were launched from the site several times a day. The derived water vapor profiles, determined at times matching the FTIR measurement times, were used to model atmospheric radiative transfer. Comparison of instrument data, all at the same spectral resolution, and model calculations, are presented along with a technique for determining adjustments to line-by-line calculation continuum models. This was a major objective of the campaign

Autoinsertion of soluble oligomers of Alzheimer's Aβ(1–42) peptide into cholesterol-containing membranes is accompanied by relocation of the sterol towards the bilayer surface

BACKGROUND: Soluble Alzheimer's Aβ oligomers autoinsert into neuronal cell membranes, contributing to the pathology of Alzheimer's Disease (AD), and elevated serum cholesterol is a risk factor for AD, but the reason is unknown. We investigated potential connections between these two observations at the membrane level by testing the hypothesis that Aβ(1–42) relocates membrane cholesterol. RESULTS: Oligomers of Aβ(1–42), but not the monomeric peptide, inserted into cholesterol-containing phosphatidylcholine monolayers with an anomalously low molecular insertion area, suggesting concurrent lipid rearrangement. Membrane neutron diffraction, including isomorphous replacement of specific lipid hydrogens with highly-scattering deuterium, showed that Aβ(1–42) insertion was accompanied by outward displacement of membrane cholesterol, towards the polar surfaces of the bilayer. Changes in the generalised polarisation of laurdan confirmed that the structural changes were associated with a functional alteration in membrane lipid order. CONCLUSION: Cholesterol is known to regulate membrane lipid order, and this can affect a wide range of membrane mechanisms, including intercellular signalling. Previously unrecognised Aβ-dependent rearrangement of the membrane sterol could have an important role in AD

An isotopic approach to partition evapotranspiration in a mixed deciduous forest

Transpiration (T) is perhaps the largest fluxes of water from the land surface to the atmosphere and is susceptible to changes in climate, land use and vegetation structure. However, predictions of future transpiration fluxes vary widely and are poorly constrained. Stable water isotopes can help expand our understanding of land–atmosphere water fluxes but are limited by a lack of observations and a poor understanding of how the isotopic composition of transpired vapour (δT) varies. Here, we present isotopic data of water vapour, terrestrial water and plant water from a deciduous forest to understand how vegetation affects water budgets and land–atmosphere water fluxes. We measured subdiurnal variations of δ18OT from three tree species and used water isotopes to partition T from evapotranspiration (ET) to quantify the role of vegetation in the local water cycle. We find that δ18OT deviated from isotopic steady‐state during the day but find no species‐specific patterns. The ratio of T to ET varied from 53% to 61% and was generally invariant during the day, indicating that diurnal evaporation and transpiration fluxes respond to similar atmospheric and micrometeorological conditions at this site. Finally, we compared the isotope‐inferred ratio of T to ET with results from another ET partitioning approach that uses eddy covariance and sap flux data. We find broad midday agreement between these two partitioning techniques, in particular, the absence of a diurnal cycle, which should encourage future ecohydrological isotope studies. Isotope‐inferred estimates of transpiration can inform land surface models and improve our understanding of land–atmosphere water fluxes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/162787/2/eco2229.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162787/1/eco2229_am.pd