Breaking ranks: the emergence of representative associations in the Irish armed forces 1989-1992

This study contexualises the relationship between the armed forces and the civil authority in Ireland using and revising the theoretical framework advanced by Huntington. It tracks the evolution of the idea of a representive body for soldiers in the late 1980s, to the setting up of statutory associations under the Defence Amendment Act 1990. The study considers Irish soldiers political agitation and their use of peaceful democratic activities to achieve their aims. It highlights the fundamental policy arguments that were made against the idea of representation for the army and positions those arguments in the study of civil-military relations. Utilising unique access to secret Department of Defence files, it reveals in-depth ideological arguments advanced by the military authories in Ireland against independent representation. This thesis provides an academic study of the establishment of PDFORRA. It answers key questions regarding the change in the position of Irish government who were categorically opposed to the idea of representation in the army. It illustrates the involvement of other agencies such as the European Organisation of Military Associations (Euromil) reveals reciprocal support by the Irish associations to other emerging groups in Spain. Accessing as yet unpublished Department of Defence files, study analyses tension between the military authorities and the government. It highlights for the first time the role of enlisted personnel in the shaping of new state structures and successfully dismmisses Huntingtons theoretical contention that enlisted personnel are of no consequence in the study of civil-military relations. It fills a gap in our understanding, identified by Finer, as to how politicisation of soldiers takes place. This thesis brings a new dimension to the discipline of civil-military relations and creates new knowledge that will enhance our understanding of an area not covered previously.

Rare variants create synthetic genome-wide associations.

Genome-wide association studies (GWAS) have now identified at least 2,000 common variants that appear associated with common diseases or related traits (http://www.genome.gov/gwastudies), hundreds of which have been convincingly replicated. It is generally thought that the associated markers reflect the effect of a nearby common (minor allele frequency >0.05) causal site, which is associated with the marker, leading to extensive resequencing efforts to find causal sites. We propose as an alternative explanation that variants much less common than the associated one may create "synthetic associations" by occurring, stochastically, more often in association with one of the alleles at the common site versus the other allele. Although synthetic associations are an obvious theoretical possibility, they have never been systematically explored as a possible explanation for GWAS findings. Here, we use simple computer simulations to show the conditions under which such synthetic associations will arise and how they may be recognized. We show that they are not only possible, but inevitable, and that under simple but reasonable genetic models, they are likely to account for or contribute to many of the recently identified signals reported in genome-wide association studies. We also illustrate the behavior of synthetic associations in real datasets by showing that rare causal mutations responsible for both hearing loss and sickle cell anemia create genome-wide significant synthetic associations, in the latter case extending over a 2.5-Mb interval encompassing scores of "blocks" of associated variants. In conclusion, uncommon or rare genetic variants can easily create synthetic associations that are credited to common variants, and this possibility requires careful consideration in the interpretation and follow up of GWAS signals.

Associations between Intake of Folate, Methionine, and Vitamins B-12, B-6 and Prostate Cancer Risk in American Veterans.

Prostate cancer (PC) is the second leading cause of cancer death in men. Recent reports suggest that excess of nutrients involved in the one-carbon metabolism pathway increases PC risk; however, empirical data are lacking. Veteran American men (272 controls and 144 PC cases) who attended the Durham Veteran American Medical Center between 2004-2009 were enrolled into a case-control study. Intake of folate, vitamin B12, B6, and methionine were measured using a food frequency questionnaire. Regression models were used to evaluate the association among one-carbon cycle nutrients, MTHFR genetic variants, and prostate cancer. Higher dietary methionine intake was associated with PC risk (OR = 2.1; 95%CI 1.1-3.9) The risk was most pronounced in men with Gleason sum <7 (OR = 2.75; 95%CI 1.32- 5.73). The association of higher methionine intake and PC risk was only apparent in men who carried at least one MTHFR A1298C allele (OR = 6.7; 95%CI = 1.6-27.8), compared to MTHFR A1298A noncarrier men (OR = 0.9; 95%CI = 0.24-3.92) (p-interaction = 0.045). There was no evidence for associations between B vitamins (folate, B12, and B6) and PC risk. Our results suggest that carrying the MTHFR A1298C variants modifies the association between high methionine intake and PC risk. Larger studies are required to validate these findings.

Novel associations of UDP-glucuronosyltransferase 2B gene variants with prostate cancer risk in a multiethnic study.

BACKGROUND: We have previously shown that a functional polymorphism of the UGT2B15 gene (rs1902023) was associated with increased risk of prostate cancer (PC). Novel functional polymorphisms of the UGT2B17 and UGT2B15 genes have been recently characterized by in vitro assays but have not been evaluated in epidemiologic studies. METHODS: Fifteen functional SNPs of the UGT2B17 and UGT2B15 genes, including cis-acting UGT2B gene SNPs, were genotyped in African American and Caucasian men (233 PC cases and 342 controls). Regression models were used to analyze the association between SNPs and PC risk. RESULTS: After adjusting for race, age and BMI, we found that six UGT2B15 SNPs (rs4148269, rs3100, rs9994887, rs13112099, rs7686914 and rs7696472) were associated with an increased risk of PC in log-additive models (p < 0.05). A SNP cis-acting on UGT2B17 and UGT2B15 expression (rs17147338) was also associated with increased risk of prostate cancer (OR = 1.65, 95% CI = 1.00-2.70); while a stronger association among men with high Gleason sum was observed for SNPs rs4148269 and rs3100. CONCLUSIONS: Although small sample size limits inference, we report novel associations between UGT2B15 and UGT2B17 variants and PC risk. These associations with PC risk in men with high Gleason sum, more frequently found in African American men, support the relevance of genetic differences in the androgen metabolism pathway, which could explain, in part, the high incidence of PC among African American men. Larger studies are required.

Associations between BMI and home, school and route environmental exposures estimated using GPS and GIS: do we see evidence of selective daily mobility bias in children?

BACKGROUND: This study examined whether objective measures of food, physical activity and built environment exposures, in home and non-home settings, contribute to children's body weight. Further, comparing GPS and GIS measures of environmental exposures along routes to and from school, we tested for evidence of selective daily mobility bias when using GPS data. METHODS: This study is a cross-sectional analysis, using objective assessments of body weight in relation to multiple environmental exposures. Data presented are from a sample of 94 school-aged children, aged 5-11 years. Children's heights and weights were measured by trained researchers, and used to calculate BMI z-scores. Participants wore a GPS device for one full week. Environmental exposures were estimated within home and school neighbourhoods, and along GIS (modelled) and GPS (actual) routes from home to school. We directly compared associations between BMI and GIS-modelled versus GPS-derived environmental exposures. The study was conducted in Mebane and Mount Airy, North Carolina, USA, in 2011. RESULTS: In adjusted regression models, greater school walkability was associated with significantly lower mean BMI. Greater home walkability was associated with increased BMI, as was greater school access to green space. Adjusted associations between BMI and route exposure characteristics were null. The use of GPS-actual route exposures did not appear to confound associations between environmental exposures and BMI in this sample. CONCLUSIONS: This study found few associations between environmental exposures in home, school and commuting domains and body weight in children. However, walkability of the school neighbourhood may be important. Of the other significant associations observed, some were in unexpected directions. Importantly, we found no evidence of selective daily mobility bias in this sample, although our study design is in need of replication in a free-living adult sample.

Fear learning circuitry is biased toward generalization of fear associations in posttraumatic stress disorder.

Fear conditioning is an established model for investigating posttraumatic stress disorder (PTSD). However, symptom triggers may vaguely resemble the initial traumatic event, differing on a variety of sensory and affective dimensions. We extended the fear-conditioning model to assess generalization of conditioned fear on fear processing neurocircuitry in PTSD. Military veterans (n=67) consisting of PTSD (n=32) and trauma-exposed comparison (n=35) groups underwent functional magnetic resonance imaging during fear conditioning to a low fear-expressing face while a neutral face was explicitly unreinforced. Stimuli that varied along a neutral-to-fearful continuum were presented before conditioning to assess baseline responses, and after conditioning to assess experience-dependent changes in neural activity. Compared with trauma-exposed controls, PTSD patients exhibited greater post-study memory distortion of the fear-conditioned stimulus toward the stimulus expressing the highest fear intensity. PTSD patients exhibited biased neural activation toward high-intensity stimuli in fusiform gyrus (P<0.02), insula (P<0.001), primary visual cortex (P<0.05), locus coeruleus (P<0.04), thalamus (P<0.01), and at the trend level in inferior frontal gyrus (P=0.07). All regions except fusiform were moderated by childhood trauma. Amygdala-calcarine (P=0.01) and amygdala-thalamus (P=0.06) functional connectivity selectively increased in PTSD patients for high-intensity stimuli after conditioning. In contrast, amygdala-ventromedial prefrontal cortex (P=0.04) connectivity selectively increased in trauma-exposed controls compared with PTSD patients for low-intensity stimuli after conditioning, representing safety learning. In summary, fear generalization in PTSD is biased toward stimuli with higher emotional intensity than the original conditioned-fear stimulus. Functional brain differences provide a putative neurobiological model for fear generalization whereby PTSD symptoms are triggered by threat cues that merely resemble the index trauma.

Low colloidal associations of aluminium and titanium in surface waters of the tropical Atlantic

The distribution of dissolved, soluble and colloidal fractions of Al and Ti was assessed by ultrafiltration studies in the upper water column of the eastern tropical North Atlantic. The dissolved fractions of both metals were found to be dominated by the soluble phase smaller than 10 kDa. The colloidal associations were very low (0.2–3.4%) for Al and not detectable for Ti. These findings are in some contrast to previous estimations for Ti and to the predominant occurrence of both metals as hydrolyzed species in seawater. However, low tendencies to form inorganic colloids can be expected, as in seawater dissolved Al and dissolved Ti are present within their inorganic solubility levels. In addition, association with functional organic groups in the colloidal phase is unlikely for both metals. Vertical distributions of the dissolved fractions showed surface maxima with up to 43 nM of Al and 157 pM of Ti, reflecting their predominant supply from atmospheric sources to the open ocean. In the surface waters, excess dissolved Al over dissolved Ti was present compared to the crustal source, indicating higher solubility and thus elevated inputs of dissolved Al from atmospheric mineral particles. At most stations, subsurface minima of Al and Ti were observed and can be ascribed to scavenging processes and/or biological uptake. The dissolved Al concentrations decreased by 80–90% from the surface maximum to the subsurface minimum. Estimated residence times in the upper 100 m of the water column ranged between 1.6 and 4 years for dissolved Al and between 14 and 17 years for dissolved Ti. The short residence times are in some contrast to the low colloidal associations of Al and Ti and the assumed role of colloids as intermediates in scavenging processes. This suggests that either the removal of both metals occurs predominantly via direct transfer of the hydrolyzed species into the particulate fraction or that the colloidal phase is rapidly turned over in the upper water column.

Zooplankton associations in a Mediterranean long-term time-series

Coastal zooplankton have been investigated since 1984 at a Long Term Ecological Research station MC (LTER-MC) in the inner Gulf of Naples (Tyrrhenian Sea, Western Mediterranean). The sampling site, located between the littoral and the open sea systems, has very active hydrography that affects plankton communities. The present work was aimed at establishing whether, in such a dynamic and variable environment, species associations and homogeneous periods could be identified as characteristic and stable features of the mesozooplankton over the period 1984–2006. Hierarchical clustering was applied to assess species associations based on a matrix of similarities between species (R-mode), and homogeneous periods based on a matrix of similarities between observations (Q-mode). The Indicator Value index [IndVal, Dufrene and Legendre (1997) Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Monogr., 67, 345–366] was calculated to identify species characterizing each period. Five taxonomic groups with well-defined composition and abundance were identified as robust associations that likely reflect different modes of community functioning. The temporal course of these associations was largely shaped by strong seasonal forcing comprising both physical and biological (e.g. trophic) signals. These associations persisted over the long term, thus indicating some stable characters in the Naples zooplankton time-series, providing evidence of resilience in communities in highly variable coastal conditions.

Macro-ecology of plankton–seabird associations in the North Pacific Ocean

In conjunction with the North Pacific Continuous Plankton Recorder program, we conducted surveys of seabirds from June 2002 to June 2007. Here, we tested the hypotheses of (i) east–west variations in coupled plankton and seabird abundance, and (ii) that surface-feeding and diving seabirds vary in their relationships to primary productivity and mesozooplankton species abundance and diversity. To test these hypotheses, we developed statistical models for 20 species of seabirds and 12 zooplankton taxonomic groups. Seabird density was highly variable between seasons, but was consistently higher in the western than eastern North Pacific. Seabird diversity was greater in the east. Zooplankton abundance did not differ between regions. We found associations at the “bulk” level between seabird density and net primary productivity, but only one association between seabirds and total zooplankton abundance or diversity. However, we found many relationships between seabird species and the abundance of different zooplankton summarized at the genus or family level. Some of these taxonomic relationships reflect direct predator–prey interactions, while others may reflect zooplankton that serve as ecological indicators of other prey, such as micronekton, upon which the birds may feed. Surface or near-surface feeding, mostly piscivorous seabirds, did not differ systematically from diving, mainly planktivorous seabirds in their zooplankton associations. Seabirds apparently respond to zooplankton taxonomic groupings more so than bulk zooplankton characteristics, such as abundance or diversity. Macro-ecological studies of remote marine ecosystems using zooplankton and seabirds as ecological indicators provide a framework for understanding and assessing spatial and temporal variations in these difficult-to-study pelagic environments.

Microsporidia-nematode associations in methane seeps reveal basal fungal parasitism in the deep sea

The deep sea is Earth’s largest habitat but little is known about the nature of deep-sea parasitism. In contrast to a few characterized cases of bacterial and protistan parasites, the existence and biological significance of deep-sea parasitic fungi is yet to be understood. Here we report the discovery of a fungus-related parasitic microsporidium, Nematocenator marisprofundi n. gen. n. sp. that infects benthic nematodes at Pacific Ocean methane seeps on the Pacific Ocean floor. This infection is species-specific and has been temporally and spatially stable over two years of sampling, indicating an ecologically consistent host-parasite interaction. A high distribution of spores in the reproductive tracts of infected males and females and their absence from host nematodes’ intestines suggests a sexual transmission strategy in contrast to the fecal-oral transmission of most microsporidia. N. marisprofundi targets the host’s body wall muscles causing cell lysis, and in severe infection even muscle filament degradation. Phylogenetic analyses placed N. marisprofundi in a novel and basal clade not closely related to any described microsporidia clade, suggesting either that microsporidia-nematode parasitism occurred early in microsporidia evolution or that host specialization occurred late in an ancient deep-sea microsporidian lineage. Our findings reveal that methane seeps support complex ecosystems involving interkingdom interactions between bacteria, nematodes, and parasitic fungi and that microsporidia parasitism exists also in the deep sea biosphere.