Analogue Methods in Palaeoecology: Using the analogue Package

Palaeoecology is an important branch of ecology that uses the subfossil remains of organisms preserved in lake, ocean and bog sediments to inform on changes in ecosystems and the environment through time. The analogue package contains functions to perform modern analogue technique (MAT) transfer functions, which can be used to predict past changes in the environment, such as climate or lake-water pH from species data. A related technique is that of analogue matching, which is concerned with identifying modern sites that are floristically and faunistically similar to fossil samples. These techniques, and others, are increasingly being used to inform public policy on environmental pollution and conservation practices. These methods and other functionality in analogue are illustrated using the Surface Waters Acidification Project diatom:pH training set and diatom counts on samples of a sediment core from the Round Loch of Glenhead, Galloway, Scotland. The paper is aimed at palaeoecologists who are familiar with the techniques described but not with R.

Spatial variations in snowpack chemistry and isotopic composition of NO3- along a nitrogen deposition gradient in West Greenland

Snowpack chemistry, nitrate stable isotopes and net deposition fluxes for the largest ice-free region in Greenland were investigated to determine whether there are spatial gradients from the ice sheet margin to the coast linked to a gradient in precipitation. Late-season snowpack was sampled in March 2011 at 8 locations within 3 lake catchments in each of 3 regions (ice sheet margin in the east, central area near Kelly Ville and the coastal zone to the west). At the coast, snowpack accumulation averaged 181 mm snow water equivalent (SWE), compared with 36 mm SWE by the ice sheet. Coastal snowpack showed significantly greater concentrations of marine salts (Na+, Cl−, other major cations), ammonium (regional means 1.4–2.7 µmol L−1), total and non-sea salt sulfate (total 1.8–7.7, non-sea salt 1.0–1.8 µmol L−1) than the two inland regions. Nitrate (1.5–2.4 µmol L−1) showed significantly lower concentrations at the coast. Despite lower concentrations, higher precipitation at the coast results in a strong deposition gradient for NO3− as well as NH4+ and non-sea salt sulfate (nss-SO42−) increasing from the inland regions to the coast (lowest at Kelly Ville 6, 4 and 3; highest at coast 9, 17 and 11 mol ha−1 yr−1 of NO3−, NH4+ and nss-SO42− respectively). The δ(15N) of snowpack NO3− shows a significant decrease from the ice sheet margin (−7.5 ‰) to the coast (−11.3 ‰). We attribute the spatial gradient of δ(15N) in SW Greenland to post-deposition processing rather than differing sources because of (1) the climatic gradient from ice sheet margin to coast, (2) within-catchment isotopic differences between terrestrial snowpack and lake-ice snowpack, and (3) similarities between fresh snow (rather than accumulated snowpack) at Kelly Ville and the coast. Hence the δ(15N) of coastal snowpack is most representative of snowfall in SW Greenland, but after deposition the effects of photolysis, volatilization and sublimation lead to enrichment of the remaining snowpack with the greatest effect in inland areas of low precipitation and high sublimation losses

Analogue Methods in Palaeoecology: Using the analogue Package

Palaeoecology is an important branch of ecology that uses the subfossil remains of organisms preserved in lake, ocean and bog sediments to inform on changes in ecosystems and the environment through time. The analogue package contains functions to perform modern analogue technique (MAT) transfer functions, which can be used to predict past changes in the environment, such as climate or lake-water pH from species data. A related technique is that of analogue matching, which is concerned with identifying modern sites that are floristically and faunistically similar to fossil samples. These techniques, and others, are increasingly being used to inform public policy on environmental pollution and conservation practices. These methods and other functionality in analogue are illustrated using the Surface Waters Acidification Project diatom:pH training set and diatom counts on samples of a sediment core from the Round Loch of Glenhead, Galloway, Scotland. The paper is aimed at palaeoecologists who are familiar with the techniques described but not with R

The Subaru-XMM-Newton Deep Survey (SXDS) VIII.: Multi-wavelength Identification, Optical/NIR Spectroscopic Properties, and Photometric Redshifts of X-ray Sources

We report the multi-wavelength identification of the X-ray sources found in the Subaru-XMM-Newton Deep Survey (SXDS) using deep imaging data covering the wavelength range between the far-UV to the mid-IR. We select a primary counterpart of each X-ray source by applying the likelihood ratio method to R-band, 3.6micron, near-UV, and 24micron source catalogs as well as matching catalogs of AGN candidates selected in 1.4GHz radio and i'-band variability surveys. Once candidates of Galactic stars, ultra-luminous X-ray sources in a nearby galaxy, and clusters of galaxies are removed there are 896 AGN candidates in the sample. We conduct spectroscopic observations of the primary counterparts with multi-object spectrographs in the optical and NIR; 65\% of the X-ray AGN candidates are spectroscopically-identified. For the remaining X-ray AGN candidates, we evaluate their photometric redshift with photometric data in 15 bands. Utilising the multi-wavelength photometric data of the large sample of X-ray selected AGNs, we evaluate the stellar masses, M*, of the host galaxies of the narrow-line AGNs. The distribution of the stellar mass is remarkably constant from z=0.1 to 4.0. The relation between M* and 2--10 keV luminosity can be explained with strong cosmological evolution of the relationship between the black hole mass and M*. We also evaluate the scatter of the UV-MIR spectral energy distribution (SED) of the X-ray AGNs as a function of X-ray luminosity and absorption to the nucleus. The scatter is compared with galaxies which have redshift and stellar mass distribution matched with the X-ray AGN. The UV-NIR SEDs of obscured X-ray AGNs are similar to those of the galaxies in the matched sample. In the NIR-MIR range, the median SEDs of X-ray AGNs are redder, but the scatter of the SEDs of the X-ray AGN broadly overlaps that of the galaxies in the matched sample.Comment: Accepted for publication in PASJ Subaru special issue. 42 pages, 22 figures. Entire contents of Tables 3, 8, 9, 10, and 11, and ASCII format tables are available from http://www.astr.tohoku.ac.jp/~akiyama/SXDS/index.htm

Two-photon spectroscopy of the biphenyl chromophore. The electronic excited states of biphenyl and fluorene below 50000 cm-1

The two-photon excitation spectra of biphenyl and fluorene in dil. soln. were measured up to 50,000 cm-1. Both spectra exhibit a medium intense band system in the range 32,000-42,000 cm-1, and a strong band above 45,000 cm-1. The lowest frequency feature is assigned to a B3 symmetry transition in biphenyl and the corresponding B2 transition in fluorene. The polarization of the higher bands leads to the assignment of 2 A states at 38,000 and 47,000 cm-1. The origin of the electronically excited states of the biphenyl chromophore is discussed by simple composite mol. considerations as well as CNDO CI calcns. The latter give a semiquant. picture of transition energies and transition probabilities for 1- and 2-photon allowed excitations. A compilation of 1-photon spectra and calcns. from the literature is included in the anal. to provide a consistent picture of the electronically excited states of the biphenyl chromophore up to 50,000 cm-1

A Bayesian palaeoenvironmental transfer function model for acidified lakes

A Bayesian approach to palaeoecological environmental reconstruction deriving from the unimodal responses generally exhibited by organisms to an environmental gradient is described. The approach uses Bayesian model selection to calculate a collection of probability-weighted, species-specific response curves (SRCs) for each taxon within a training set, with an explicit treatment for zero abundances. These SRCs are used to reconstruct the environmental variable from sub-fossilised assemblages. The approach enables a substantial increase in computational efficiency (several orders of magnitude) over existing Bayesian methodologies. The model is developed from the Surface Water Acidification Programme (SWAP) training set and is demonstrated to exhibit comparable predictive power to existing Weighted Averaging and Maximum Likelihood methodologies, though with improvements in bias; the additional explanatory power of the Bayesian approach lies in an explicit calculation of uncertainty for each individual reconstruction. The model is applied to reconstruct the Holocene acidification history of the Round Loch of Glenhead, including a reconstruction of recent recovery derived from sediment trap data.The Bayesian reconstructions display similar trends to conventional (Weighted Averaging Partial Least Squares) reconstructions but provide a better reconstruction of extreme pH and are more sensitive to small changes in diatom assemblages. The validity of the posteriors as an apparently meaningful representation of assemblage-specific uncertainty and the high computational efficiency of the approach open up the possibility of highly constrained multiproxy reconstructions

A continuous infusion of a minor histocompatibility antigen-immunodominant peptide induces a delay of male skin graft rejection.

We previously reported that an inhibition of antigen-specific Interferon-gamma release and cytotoxicity occurs after a continuous infusion of an HY immunodominant peptide although this treatment is not able to cause a significant delay of male skin grafts rejection. In vivo administration of high doses of an HY peptide, through mini-osmotic pumps, in naïve female mice was used to study the effects on the male skin grafts rejection. A continuous infusion of 1mg of an HY peptide induces a significant delay of male skin graft rejection. In vitro HY-specific Interferon-gamma release was inhibited adding peptide-specific suppressor cells: the ability to inhibit Interferon-gamma release was evident when two HY peptides were present on the same dendritic cells indicating that the suppressor cells exert "linked-suppression". The phenotype of the suppressor cells is CD8(+)CD28(-) and these cells express more CD62 ligand and FOXP3 than controls. Suppressor cells were able to cause a significant delay of rejection of male skin grafts when injected in naive female mice. The inhibitory effects of these suppressor cells seem to be due to the impairment of antigen presentation; down-regulation of B7 molecules on dendritic cells occurred. Taken all together, our data demonstrate that a continuous infusion of an immunodominant HY peptide induces a T CD8 suppressor subset able to inhibit immune responses to male tissues and cells

Influence of production variables and starting material on charcoal stable isotopic and molecular characteristics

We present a systematic study on the effect of starting species, gas composition, temperature, particle size and duration of heating upon the molecular and stable isotope composition of high density (mangrove) and low density (pine) wood. In both pine and mangrove, charcoal was depleted in o13C relative to the starting wood by up to 1.6% and 0.8%, respectively. This is attributed predominantly to the progressive loss of isotopically heavier polysaccharides, and kinetic effects of aromatization during heating. However, the pattern of o13C change was dependant upon both starting species and atmosphere, with different structural changes associated with charcoal production from each wood type elucidated by Solid-State o13C Nuclear Magnetic Resonance Spectroscopy. These are particularly evident at lower temperatures, where variation in the oxygen content of the production atmosphere results in differences in the thermal degradation of cellulose and lignin. It is concluded that production of charcoal from separate species in identical conditions, or from a single sample exposed to different production variables, can result in significantly different o13C of the resulting material, relative to the initial wood. These results have implications for the use of charcoal isotope composition to infer past environmental change

Defining restoration targets for acidified upland lakes using diatom and cladoceran sub-fossil remains and the modern analogue technique

Evaluating recovery of acidified lakes towards a target based on their pre-acidification status is a difficult task as there are very few biological records for these remote upland systems. The analogue matching approach can be used to identify modern analogues for the pre-acidification status of lakes using the sub-fossil remains of diatoms and Cladocera, which can be used as recovery targets. An 83-lake modern training set was created, with full diatom, cladoceran, hydrochemistry and catchment data for each lake. Fossil samples from 10 lakes of the UK Acid Waters Monitoring Network (UKAWMN) were chosen to represent pre-acidification conditions in those lakes. The closest analogues in the modern training set were identified for each fossil sample by means of the squared chord distance measure. The distributions of the Cladocera in the training set were analysed using a range of multivariate statistical technique. Individual cladoceran species response curves for selected environmental determinands were calculated. A 163-lake diatom training set has been compiled from existing data holdings and the patterns in the data were explored using direct ordination methods. A comparison with the diatom training set from the Surface Waters Acidification Project is also made. Close modern analogues were identified for 8 UKAWMN lakes. The majority of these modern analogues are located in North and Northwest Scotland; areas of low sulphur and nitrogen deposition. Comparison of the hydrochemical characteristics of the UKAWMN lakes to those of the modern analogues showed that the modern analogues had higher lake water pH and alkalinity levels and lower aluminium concentrations. Ionic strength and calcium concentrations in the analogue lakes were similar to observed values in the UKAWMN lakes. These results indicate that the analogue matching approach using diatom and cladoceran remains is a simple, robust and reliable method of identifying modern analogues for acidified lakes in upland areas of the UK