Distribution and status of the Red Squirrel (Sciurus vulgaris) and Grey Squirrel (Sciurus carolinensis) in Ireland

The distributions of the Red and Grey Squirrel were surveyed in Northern Ireland and the Republic of Ireland between 1994 and 1996. Survey methods differed between the two studies. In the former, all suitable habitat, of at least 15 ha, was inspected for species presence or absence. In the Republic, data were gathered through questionnaires to governmental and independent wildlife bodies. The combined results indicate that the Red Squirrel remains widespread and locally abundant, and is present in all but two counties. The Grey Squirrel is now more widespread than ever before, and can be found in 22 of the 32 counties. Its range expansion has varied from 0 km/yr to an estimated 13.4 km/yr, as various geographical features, principally rivers, have hindered its progress in certain directions.

VLT DETECTION OF A RED SUPERGIANT PROGENITOR OF THE TYPE II-P SUPERNOVA 2008bk

We report the identification of a source coincident with the position of the nearby Type II-P supernova (SN) 2008bk in high-quality optical and near-infrared preexplosion images from the ESO Very Large Telescope (VLT). The SN position in the optical and near-infrared preexplosion images is identified to within about +/- 70 and +/- 40 mas, respectively, using postexplosion-band images obtained with the NAOS CONICA adaptive optics system K-s on the VLT. The preexplosion source detected in four different bands is precisely coincident with SN 2008bk and is consistent with being dominated by a single point source. We determine the nature of the point source using the STARS stellar evolutionary models and find that its colors and luminosity are consistent with the source being a red supergiant progenitor of SN 2008bk with an initial mass of 8.5 +/- 1.0 M-circle dot.

SN 2004A: another type II-P supernova with a red supergiant progenitor

We present a monitoring study of SN 2004A and probable discovery of a progenitor star in pre-explosion Hubble Space Telescope (HST) images. The photometric and spectroscopic monitoring of SN 2004A show that it was a normal Type II-P which was discovered in NGC 6207 about two weeks after explosion. We compare SN 2004A to the similar Type II-P SN 1999em and estimate an explosion epoch of 2004 January 6. We also calculate three new distances to NGC 6207 of 21.0 +/- 4.3, 21.4 +/- 3.5 and 25.1 +/- 1.7 Mpc. The former was calculated using the Standard Candle Method (SCM) for SNe II-P, and the latter two from the brightest supergiants method (BSM). We combine these three distances with existing kinematic distances, to derive a mean value of 20.3 +/- 3.4 Mpc. Using this distance, we estimate that the ejected nickel mass in the explosion is 0.046(-0.017)(+0.031) M-circle dot. The progenitor of SN 2004A is identified in pre-explosion WFPC2 F814W images with a magnitude of m(F814W) = 24.3 +/- 0.3, but is below the detection limit of the F606W images. We show that this was likely a red supergiant (RSG) with a mass of 9(-2)(+3) M-circle dot. The object is detected at 4.7 sigma above the background noise. Even if this detection is spurious, the 5 sigma upper limit would give a robust upper mass limit of 12M(circle dot) for a RSG progenitor. These initial masses are very similar to those of two previously identified RSG progenitors of the Type II-P SNe 2004gd (8(-2)(+4) M circle dot) and 2005cs (9(-2)(+3) M-circle dot).

A novel Kazal-type trypsin inhibitor from the skin secretion of the Central American red-eyed leaf frog, Agalychnis callidryas.

The chemical complexity of the defensive skin secretion of the red-eyed leaf frog, (Agalychnis callidryas), has not been elucidated in detail. During a systematic study of the skin secretion peptidomes of phyllomedusine frogs, we discovered a novel Kazal-type protein with potent trypsin inhibitory activity (Ki = 1.9 nM) that displays the highest degree of structural similarity with Kazal proteins from bony fishes. The protein was located in reverse-phase HPLC fractions following a screen of such for trypsin inhibition and subsequent partial Edman degradation of the peak active fraction derived the sequence: ATKPR-QYIVL-PRILRPV-GT. The molecular mass of the major component in this fraction was established by MALDI-TOF MS as 5893.09 Da. This partial sequence (assuming blank cycles to be Cys residues) was used to design a degenerate primer pool that was employed successfully in RACE-PCR to clone homologous precursor-encoding cDNA that encoded a mature Kazal protein of 52 amino acid residues with a computed molecular mass of 5892.82 Da. The protein was named A. callidryas Kazal trypsin inhibitor (ACKTI). BLAST analysis revealed that ACKTI contained a canonical Kazal motif (C-x(7)-C-x(6)-Y-x(3)-C-x(2,3)-C). This novel amphibian skin Kazal trypsin inhibitor adds to the spectrum of trypsin inhibitors of Kunitz- and Bowman Birk-type reported from this amphibian source.

A novel dual-fluorescence strategy for functionally validating microRNA targets in 3-prime untranslated regions: regulation of the inward rectifier potassium channel Kir2.1 by miR-212.

Gene targeting by microRNAs is important in health and disease. We developed a functional assay for identifying microRNA targets and applied it to the K+ channel Kir2.1 (KCNJ2) which is dysregulated in cardiac and vascular disorders. The 3'UTR was inserted downstream of the mCherry red fluorescent protein coding sequence in a mammalian expression plasmid. MicroRNA sequences were inserted into the pSM30 expression vector which provides enhanced green fluorescent protein as an indicator of microRNA expression. HEK293 cells were co-transfected with the mCherry-3'UTR plasmid and a pSM30-based plasmid with a microRNA insert. The principle of the assay is that functional targeting of the 3'UTR by the microRNA results in a decrease in the red/green fluorescence intensity ratio as determined by automated image analysis. The method was validated with miR-1, a known downregulator of Kir2.1 expression, and was used to investigate targeting of the Kir2.1 3'UTR by miR-212. Red/green ratio was lower in miR-212-expressing cells compared to non-targeting controls, an effect that was attenuated by mutating the predicted target site. MiR-212 also reduced inward rectifier current and Kir2.1 protein in HeLa cells. This novel assay has several advantages over traditional luciferase-based assays including larger sample size, amenability to time course studies and adaptability to high-throughput screening.

Red-shifts and red herrings in geographical ecology

I draw attention to the need for ecologists to take spatial structure into account more seriously in hypothesis testing. If spatial autocorrelation is ignored, as it usually is, then analyses of ecological patterns in terms of environmental factors can produce very misleading results. This is demonstrated using synthetic but realistic spatial patterns with known spatial properties which are subjected to classical correlation and multiple regression analyses. Correlation between an autocorrelated response variable and each of a set of explanatory variables is strongly biased in favour of those explanatory variables that are highly autocorrelated - the expected magnitude of the correlation coefficient increases with autocorrelation even if the spatial patterns are completely independent. Similarly, multiple regression analysis finds highly autocorrelated explanatory variables "significant" much more frequently than it should. The chances of mistakenly identifying a "significant" slope across an autocorrelated pattern is very high if classical regression is used. Consequently, under these circumstances strongly autocorrelated environmental factors reported in the literature as associated with ecological patterns may not actually be significant. It is likely that these factors wrongly described as important constitute a red-shifted subset of the set of potential explanations, and that more spatially discontinuous factors (those with bluer spectra) are actually relatively more important than their present status suggests. There is much that ecologists can do to improve on this situation. I discuss various approaches to the problem of spatial autocorrelation from the literature and present a randomisation test for the association of two spatial patterns which has advantages over currently available methods.

Lead contamination and associated disease in captive and reintroduced red kites Milvus milvus in England

Since 1989, a red kite Milvus milvus reintroduction programme has been underway in the United Kingdom, with 4-6 week old nestlings brought into captivity and held for 6-8 weeks before reintroduction. As scavengers, red kites may consume unretrieved game, and ingest shot or lead (Pb) fragments in their prey's flesh. We evaluated exposure to Pb in captive and wild red kites by taking blood samples from 125 captive young red kites prior to release, through analysing 264 pellets (regurgitated by wild birds) collected from under a roost site, and analysing Pb concentrations in livers and/or bones of 87 red kites found dead between 1995 and 2003. Lead isotope analyses of livers were also conducted in an effort to identify Pb exposure routes. Forty-six (36.8%) kites sampled prior to release had elevated blood Pb concentrations (201-3340 microg l(-1)). The source of this Pb was probably small fragments of lead ammunition in the carcasses of birds or mammals either fed to the nestlings by their parents or, more likely, subsequently whilst in captivity. Once released, kites were also exposed to lead shot in their food, and a minimum of 1.5-2.3% of regurgitated pellets contained Pb gunshot. Seven of 44 red kites found dead or that were captured sick and died within a few days had elevated (>6 mg kg(-1) dry weight [d.w.]) liver Pb concentrations, and six of these (14%) had concentrations of >15 mg kg(-1) d.w., compatible with fatal Pb poisoning. Post-mortem analyses indicated that two of these birds had died of other causes (poisoning by rodenticide and a banned agricultural pesticide); the remaining four (9%) probably died of Pb poisoning. Bone samples from 86 red kites showed a skewed distribution of Pb concentration, and 18 samples (21%) had Pb concentrations >20 mg kg(-1) d.w., indicating elevated exposure to Pb at some stage in the birds' life. Lead isotopic signatures (Pb (208/206); Pb (206/207)) in liver samples of the majority of kites were compatible with those found in lead shot extracted from regurgitated pellets. Lead isotope ratios found in the livers of kites with very low Pb concentrations were distinct from UK petrol Pb isotopic signatures, indicating that birds were exposed to little residual petrol Pb. We conclude that the primary source of Pb to which red kites are exposed is lead ammunition (shotgun pellets or rifle bullets), or fragments thereof, in their food sources; in some cases exposure appears sufficient to be fatal. We make recommendations to reduce Pb poisoning in both captive and wild red kites and other scavenging species.

Red and dead:The progenitor of SN 2012aw in M95

Core-collapse supernovae (SNe) are the spectacular finale to massive stellar evolution. In this Letter, we identify a progenitor for the nearby core-collapse SN 2012aw in both ground based near-infrared, and space based optical pre-explosion imaging. The SN itself appears to be a normal Type II Plateau event, reaching a bolometric luminosity of 10$^{42}$ erg s$^{-1}$ and photospheric velocities of $\sim$11,000 \kms\ from the position of the H$\beta$ P-Cygni minimum in the early SN spectra. We use an adaptive optics image to show that the SN is coincident to within 27 mas with a faint, red source in pre-explosion HST+WFPC2, VLT+ISAAC and NTT+SOFI images. The source has magnitudes $F555W$=26.70$\pm$0.06, $F814W$=23.39$\pm$0.02, $J$=21.1$\pm$0.2, $K$=19.1$\pm$0.4, which when compared to a grid of stellar models best matches a red supergiant. Interestingly, the spectral energy distribution of the progenitor also implies an extinction of $A_V>$1.2 mag, whereas the SN itself does not appear to be significantly extinguished. We interpret this as evidence for the destruction of dust in the SN explosion. The progenitor candidate has a luminosity between 5.0 and 5.6 log L/\lsun, corresponding to a ZAMS mass between 14 and 26 \msun\ (depending on $A_V$), which would make this one of the most massive progenitors found for a core-collapse SN to date.

AcT-2: A Novel Myotropic and Antimicrobial Type 2 Tryptophyllin from the Skin Secretion of the Central American Red-Eyed Leaf Frog, Agalychnis callidryas

Tryptophyllins are a diverse family of amphibian peptides originally found in extracts of phyllomedusine frog skin by chemical means. Their biological activities remain obscure. Here we describe the isolation and preliminary pharmacological characterization of a novel type 2 tryptophyllin, named AcT-2, from the skin secretion of the red-eyed leaf frog, Agalychnis callidryas. The peptide was initially identified during smooth muscle pharmacological screening of skin secretion HPLC fractions and the unique primary structure—GMRPPWF-NH2—was established by both Edman degradation and electrospray MS/MS fragmentation sequencing. A. cDNA encoding the biosynthetic precursor of AcT-2 was successfully cloned from a skin secretion-derived cDNA library by means of RACE PCR and this contained an open-reading frame consisting of 62 amino acid residues with a single AcT-2 encoding sequence located towards the C-terminus. A synthetic replicate of AcT-2 was found to relax arterial smooth muscle (EC50 = 5.1 nM) and to contract rat urinary bladder smooth muscle (EC50 = 9.3 μM). The peptide could also inhibit the growth of the microorganisms, Staphylococcus aureus, (MIC = 256 mg/L) Escherichia coli (MIC = 512 mg/L), and Candida albicans (128 mg/L). AcT-2 is thus the first amphibian skin tryptophyllin found to possess both myotropic and antimicrobial activities.

An optimized stereo vision implementation for embedded systems: application to RGB and Infra-Red images

The aim of this paper is to demonstrate the applicability and the effectiveness of a computationally demanding stereo matching algorithm in different lowcost and low-complexity embedded devices, by focusing on the analysis of timing and image quality performances. Various optimizations have been implemented to allow its deployment on specific hardware architectures while decreasing memory and processing time requirements: (1) reduction of color channel information and resolution for input images, (2) low-level software optimizations such as parallel computation, replacement of function calls or loop unrolling, (3) reduction of redundant data structures and internal data representation. The feasibility of a stereovision system on a low cost platform is evaluated by using standard datasets and images taken from Infra-Red (IR) cameras. Analysis of the resulting disparity map accuracy with respect to a full-size dataset is performed as well as the testing of suboptimal solutions

PS1-10afx at z = 1.388: Pan-STARRS1 Discovery of a New Type of Superluminous Supernova

We present the Pan-STARRS1 discovery of PS1-10afx, a unique hydrogen-deficient superluminous supernova (SLSN) at redshift z = 1.388. The light curve peaked at z P1 = 21.7 mag, making PS1-10afx comparable to the most luminous known SNe, with Mu = -22.3 mag. Our extensive optical and near-infrared observations indicate that the bolometric light curve of PS1-10afx rose on the unusually fast timescale of ~12 days to the extraordinary peak luminosity of 4.1 × 1044 erg s-1 (M bol = -22.8 mag) and subsequently faded rapidly. Equally important, the spectral energy distribution is unusually red for an SLSN, with a color temperature of ~6800 K near maximum light, in contrast to previous hydrogen-poor SLSNe, which are bright in the ultraviolet (UV). The spectra more closely resemble those of a normal SN Ic than any known SLSN, with a photospheric velocity of ~11, 000 km s-1 and evidence for line blanketing in the rest-frame UV. Despite the fast rise, these parameters imply a very large emitting radius (gsim 5 × 1015 cm). We demonstrate that no existing theoretical model can satisfactorily explain this combination of properties: (1) a nickel-powered light curve cannot match the combination of high peak luminosity with the fast timescale; (2) models powered by the spindown energy of a rapidly rotating magnetar predict significantly hotter and faster ejecta; and (3) models invoking shock breakout through a dense circumstellar medium cannot explain the observed spectra or color evolution. The host galaxy is well detected in pre-explosion imaging with a luminosity near L*, a star formation rate of ~15 M ⊙ yr-1, and is fairly massive (~2 × 1010 M ⊙), with a stellar population age of ~108 yr, also in contrast to the young dwarf hosts of known hydrogen-poor SLSNe. PS1-10afx is distinct from known examples of SLSNe in its spectra, colors, light-curve shape, and host galaxy properties, suggesting that it resulted from a different channel than other hydrogen-poor SLSNe.

Atmospheric cold plasma process for vegetable leaf decontamination: A feasibility study on radicchio (red chicory, Cichorium intybus L.)

Cold plasma is an emerging non-thermal processing technology that could be used for large scale leaf decontamination as an alternative to chlorine washing. In this study the effect of an atmospheric cold plasma apparatus (air DBD, 15 kV) on the safety, antioxidant activity and quality of radicchio (red chicory, Cichorium intybus L.) was investigated after 15 and 30 min of treatment (in afterglow at 70 mm from the discharge, at 22 °C and 60% of RH) and during storage. Escherichia coli O157:H7 inoculated on radicchio leaves was significantly reduced after 15 min cold plasma treatment (-1.35 log MPN/cm²). However, a 30 min plasma treatment was necessary to achieve a significant reduction of Listeria monocytogenes counts (-2.2 log CFU/cm²). Immediately after cold plasma treatment, no significant effects emerged in terms of antioxidant activity assessed by the ABTS and ORAC assay and external appearance of the radicchio leaves. Significant changes between treated and untreated radicchio leaves are quality defects based on the cold plasma treatment. Atmospheric cold plasma appears to be a promising processing technology for the decontamination of leafy vegetables although some criticalities, that emerged during storage, need to be considered in future studies.

Bauxite residue (Red mud) as a pulverised fuel ash substitute in the manufacture of lightweight aggregate

This study looked at the potential of bauxite residue or red mud to be used in the manufacture of lightweight aggregate in replacement of pulverised fuel ash (PFA), commonly used as a way of recycling problematic wastes. The percentage replacements of red mud with PFA were as follows: 25, 31, 38, 44 and 50%. These were blended in a mix with waste excavated clay and sewage sludge – all from the Chongqing municipality in China. Lightweight pellets were produced using a Trefoil rotary kiln and were sintered to 1200 °C. Results showed that 44 % bauxite residue replacement produced lightweight pellets with the highest compressive strength, highest density and largest water holding capacity. This would be expected in materials with a low level of silicates, which causes insufficient glass phase viscosity and therefore poor bloating during firing; producing an aggregate with a higher density but with open pores that allowed for larger water absorption. All ratios of red mud aggregates were significantly reduced in pH after firing to around pH 8, and this reduced the leachability of the aggregates to levels below those set by the European landfill directive (2003/33/EC).

Detection of mineralized structures in very early stages of development of Marine Teleostei using a modified Alcian blue-Alizarin red double staining technique for bone and cartilage

We have developed a procedure for staining cartilage and bone in fish larvae as small as 2 mm (notochord length), for which standard alcian blue/alizarin red procedures did not give positive and/or consistent results. Small calcified structures only 100-200 pm in length can be clearly visualized. The method is suitable for both ontogenic studies during early stages of skeletal development in most marine fishes (e.g., Sparus aurata L., Solea senegalensis Kaup), whose larvae at hatching are often only a few millimeters long and for detecting skeletal abnormalities in small larvae. This procedure can also be used for specimens that have been preserved in 1000/0 ethanol for up to two years.