Population enumeration and assessing conservation status in a widespread amphibian: A case study of Rana temporaria in Ireland

Global amphibian declines are a major element of the current biodiversity crisis. Monitoring changes in the distribution and abundance of target species is a basic component in conservation decision making and requires robust and repeatable sampling. For EU member states, surveillance of designated species, including the common frog Rana temporaria, is a formal requirement of the 'EC Habitats & Species Directive'. We deployed established methods for estimating frog population density at local water bodies and extrapolated these to the national and ecoregion scale. Spawn occurred at 49.4% of water bodies and 70.1% of independent 500-m survey squares. Using spawn mat area, we estimated the number of adult breeding females and subsequently the total population assuming a sex ratio of 1:1. A negative binomial model suggested that mean frog density was 23.5 frogsha [95% confidence interval (CI) 14.9-44.0] equating to 196M frogs (95%CI 124M-367M) throughout Ireland. A total of 86% of frogs bred in drainage ditches, which were a notably common feature of the landscape. The recorded distribution of the species did not change significantly between the last Article 17 reporting period (1993-2006) and the current period (2007-2011) throughout the Republic of Ireland. Recording effort was markedly lower in Northern Ireland, which led to an apparent decline in the recorded distribution. We highlight the need to coordinate biological surveys between adjacent political jurisdictions that share a common ecoregion to avoid apparent disparities in the quality of distributional information. Power analysis suggested that a reduced sample of 40-50 survey squares is sufficient to detect a 30% decline (consistent with the International Union for Conservation of Nature Category of 'Vulnerable') at 80% power providing guidance for minimizing future survey effort. Our results provin assessments for R. temporaria and other clump-spawning amphibians. 2013 The Zoological Society of London.

Risk of Several Cancers is Higher in Urban Areas after Adjusting for Socioeconomic Status. Results from a Two-Country Population-Based Study of 18 Common Cancers

Some studies suggest that there are urban-rural variations in cancer incidence but whether these simply reflect urban-rural socioeconomic variation is unclear. We investigated whether there were urban-rural variations in the incidence of 18 cancers, after adjusting for socioeconomic status. Cancers diagnosed between 1995 and 2007 were extracted from the population-based National Cancer Registry Ireland and Northern Ireland Cancer Registry and categorised by urban-rural status, based on population density of area of residence at diagnosis (rural 15 people per hectare). Relative risks (RR) were calculated by negative binomial regression, adjusting for age, country and three area-based markers of socioeconomic status. Risks were significantly higher in both sexes in urban than rural residents with head and neck (males RR urban vs. rural = 1.53, 95 % CI 1.42-1.64; females RR = 1.29, 95 % CI 1.15-1.45), esophageal (males 1.21, 1.11-1.31; females 1.21, 1.08-1.35), stomach (males 1.36, 1.27-1.46; females 1.19, 1.08-1.30), colorectal (males 1.14, 1.09-1.18; females 1.04, 1.00-1.09), lung (males 1.54, 1.47-1.61; females 1.74, 1.65-1.84), non-melanoma skin (males 1.13, 1.10-1.17; females 1.23, 1.19-1.27) and bladder (males 1.30, 1.21-1.39; females 1.31, 1.17-1.46) cancers. Risks of breast, cervical, kidney and brain cancer were significantly higher in females in urban areas. Prostate cancer risk was higher in rural areas (0.94, 0.90-0.97). Other cancers showed no significant urban-rural differences. After adjusting for socioeconomic variation, urban-rural differences were evident for 12 of 18 cancers. Variations in healthcare utilization and known risk factors likely explain some of the observed associations. Explanations for others are unclear and, in the interests of equity, warrant further investigation. © 2014 The New York Academy of Medicine.

mfx: Marginal Effects, Odds Ratios and Incidence Rate Ratios for GLMs

Estimates probit, logit, Poisson, negative binomial, and beta regression models, returning their marginal effects, odds ratios, or incidence rate ratios as an output.

Excess mortality in Type 1 diabetes diagnosed in childhood and adolescence: a systematic review of population-based cohorts

Aims: Systematic review of mortality in childhood-/adolescent-diagnosed Type 1 diabetes and examination of factors explaining the mortality variation between studies. 
Methods: Relevant studies were identified from systematic searches of MEDLINE and EMBASE. Observed and expected numbers of deaths were extracted, and standardised mortality ratios (SMRs) and 95 % confidence intervals (CIs) were calculated. Negative binomial regression was used to investigate association between mortality and study/country characteristics.
Results: Thirteen relevant publications with mortality data were identified describing 23 independent studies. SMRs varied markedly ranging from 0 to 854 (chi-squared = 70.68,df = 21, p<0.0001). Significant associations were observed between SMR and mid-year of follow-up [incidence rate ratio (IRR) 0.95, 95 % CI 0.91–0.99 equivalent to a 5 % decrease per year], between SMR and infant mortality rate (IRR 1.07, 95 % CI 1.02–1.12, a 7 % increase for each death per 1,000 live births) and, after omitting an outlier, between SMR and health expenditure as a percentage of gross domestic product (GDP) (IRR 0.79, 95 % CI 0.68–0.93, a 21 % decrease for each one percent increase in GDP). No relationship was detected between SMR and a country’s childhood diabetes incidence rate or GDP.
Conclusions: Excess mortality in childhood-/adolescent diagnosed Type 1 diabetes is apparent across countries worldwide. Excesses were less marked in more recent studies and in countries with lower infant mortality and higher health expenditure.

Truncated estrogen receptor alpha 46-kDa isoform in human endothelial cells: relationship to acute activation of nitric oxide synthase.

Background Estrogen acutely activates endothelial nitric oxide synthase (eNOS). However, the identity of the receptors involved in this rapid response remains unclear. Methods and Results We detected an estrogen receptor (ER) transcript in human endothelial cells that encodes a truncated 46-kDa ER (1a-hER-46). A corresponding 46-kDa ER protein was identified in endothelial cell lysates. Transfection of cDNAs encoding the full-length ER (ER-66) and 1a-hER-46 resulted in appropriately sized recombinant proteins identified by anti-ER antibodies. Confocal microscopy revealed that a proportion of both ER-66 and hER-46 was localized outside the nucleus and mediated specific cell-surface binding of estrogen as assessed by FITC-conjugated, BSA-estrogen binding studies. Both ER isoforms colocalized with eNOS and mediated acute activation of eNOS in response to estrogen stimulation. However, estrogen-stimulated transcriptional activation mediated by 1a-hER-46 was much less than with ER-66. Furthermore, 1a-hER-46 inhibited classical hER-66 mediated transcriptional activation in a dominant-negative fashion. Conclusions These findings suggest that expression of an alternatively spliced, truncated ER isoform in human endothelial cells confers a unique ability to mediate acute but not transcriptional responses to estrogen.

A novel shrinkage technique based on the normal inverse Gaussian density model

This paper proposes a novel image denoising technique based on the normal inverse Gaussian (NIG) density model using an extended non-negative sparse coding (NNSC) algorithm proposed by us. This algorithm can converge to feature basis vectors, which behave in the locality and orientation in spatial and frequency domain. Here, we demonstrate that the NIG density provides a very good fitness to the non-negative sparse data. In the denoising process, by exploiting a NIG-based maximum a posteriori estimator (MAP) of an image corrupted by additive Gaussian noise, the noise can be reduced successfully. This shrinkage technique, also referred to as the NNSC shrinkage technique, is self-adaptive to the statistical properties of image data. This denoising method is evaluated by values of the normalized signal to noise rate (SNR). Experimental results show that the NNSC shrinkage approach is indeed efficient and effective in denoising. Otherwise, we also compare the effectiveness of the NNSC shrinkage method with methods of standard sparse coding shrinkage, wavelet-based shrinkage and the Wiener filter. The simulation results show that our method outperforms the three kinds of denoising approaches mentioned above.

A Tower-Shadow Model for Wind Turbines Using a Wavelet-Prony Method

The increasing penetration of wind generation on the Island of Ireland has been accompanied by close investigation of low-frequency pulsations contained within active power flow. A primary concern is excitation of low-frequency oscillation modes already present on the system, particularly the 0.75 Hz mode as a consequence of interconnection between the Northern and Southern power system networks. In order to determine whether the prevalence of wind generation has a negative effect (excites modes) or positive impact (damping of modes) on the power system, oscillations must be measured and characterised. Using time – frequency methods, this paper presents work that has been conducted to extract features from low-frequency active power pulsations to determine the composition of oscillatory modes which may impact on dynamic stability. The paper proposes a combined wavelet-Prony method to extract modal components and determine damping factors. The method is exemplified using real data obtained from wind farm measurements.

Electron attachment to SF(6) and lifetimes of SF(6)(-) negative ions

We study the process of low-energy electron capture by the SF(6) molecule. Our approach is based on the model of Gauyacq and Herzenberg [J. P. Gauyacq and A. Herzenberg, J. Phys. B 17, 1155 (1984)] in which the electron motion is coupled to the fully symmetric vibrational mode through a weakly bound or virtual s state. By tuning the two free parameters of the model, we achieve an accurate description of the measured electron attachment cross section and good agreement with vibrational excitation cross sections of the fully symmetric mode. An extension of the model provides a limit on the characteristic time of intramolecular vibrational relaxation in highly excited SF(6)(-). By evaluating the total vibrational spectrum density of SF(6)(-), we estimate the widths of the vibrational Feshbach resonances of the long-lived negative ion. We also analyze the possible distribution of the widths and its effect on the lifetime measurements, and investigate nonexponential decay features in metastable SF(6)(-).

Chemical etching of optical fibre tips - experiment and model

The formation of chemically etched fibre tips for use in optical scanning probe microscopy is addressed. For tips formed at a cleaved fibre end in the bulk of a buffered HF acid solution the morphological features (tip height, cone angle) are found to depend strongly on the temperature and etchant composition. The tip formation process is analysed and explained in terms of a simple model in which the only pertinent physical parameters are the fibre core diameter and etch rates of the fibre core and cladding. The etch rates are determined in separate experiments as a function of temperature (in the range 24-50 degreesC) for etchant solutions of de ionised water: 50% HF acid: 40% NH4F in the volume ratio 1 : 1 : X for X=2, 4 and 6, and used in the model to yield a correct description of the experimental tip cone angles. The model is successfully extended to the intriguing case of negative tip formation which initiates in a normal, positive tip structure. By contrast, tip formation in the meniscus region of a bare fibre/etchant/organic solvent system is found to be independent of etchant composition and temperature. (C) 2000 Elsevier Science B.V. All rights reserved.

Murine model of autosomal dominant retinitis pigmentosa generated by targeted deletion at codon 307 of the rds-peripherin gene

We introduced a targeted single base deletion at codon 307 of the rds-peripherin gene in mice, similar mutations being known to cause autosomal dominant retinitis pigmentosa (RP) in man. Histopathological and electroretinographic analysis indicate that the retinopathy in mice homozygous for the codon 307 mutation appears more rapid than that in the naturally occurring null mutant, the rds(-/-) mouse, suggesting that the rds-307 mutation displays a dominant negative phenotype in combination with that due to haplosufficiency. RP is the most prevalent cause of registered visual handicap in those of working age in developed countries, the 50 or so mutations so far identified within the RDS-peripherin gene accounting for up to 10% of dominant cases of the disease. Given the sequence homologies that exist between the murine rds-peripherin and the human RDS-peripherin gene, this disease model, the first to be generated for peripherin-based RP using gene targeting techniques, should in principle be of value in the work-up in mice of therapeutics capable of targeting transcripts derived from the human gene.

Political Violence and Child Adjustment in Northern Ireland: Testing Pathways in a Social-Ecological Model Including Single- and Two-Parent Families

Moving beyond simply documenting that political violence negatively impacts children, we tested a social ecological hypothesis for relations between political violence and child outcomes. Participants were 700 mother child (M = 12.1 years, SD = 1.8) dyads from 18 working-class, socially deprived areas in Belfast, Northern Ireland, including single- and two-parent families. Sectarian community violence was associated with elevated family conflict and children's reduced security about multiple aspects of their social environment (i.e., family, parent child relations, and community), with links to child adjustment problems and reductions in prosocial behavior. By comparison, and consistent with expectations, links with negative family processes, child regulatory problems, and child outcomes were less consistent for nonsectarian community violence. Support was found for a social ecological model for relations between political violence and child outcomes among both single- and two-parent families, with evidence that emotional security and adjustment problems were more negatively affected in single-parent families. The implications for understanding social ecologies of political violence and children's functioning are discussed.

Asymptotic layer-type model of high pressure direct current glow discharge in electronegative gases

Here a self-consistent one-dimensional continuum model is presented for a narrow gap plane-parallel dc glow discharge. The governing equations consist of continuity and momentum equations for positive and negative ions and electrons coupled with Poisson's equation. A singular perturbation method is developed for the analysis of high pressure dc glow discharge. The kinetic processes of the ionization, electron attachment, and ion-ion recombination are included in the model. Explicit results are obtained for the asymptotic limits: delta=(r(D)/L)(2)--> 0, omega=(r(S)/L)(2)--> 0, where r(D) is the Debye radius, r(S) is recombination length, and L is the gap length. The discharge gap divides naturally into four layers with multiple space scales: anode fall region, positive column, transitional region, cathode fall region and diffusion layer adjacent to the cathode surface, its formation is discussed. The effects of the gas pressure, gap spacing and dc voltage on the electrical properties of the layers and its dimension are investigated. (C) 2000 American Institute of Physics. [S0021-8979(00)00813-6].