Airborne thermography and ground geophysical investigation for detecting shallow ground disturbance under vegetation

This thesis discusses the potential of airborne thermal prospection for detecting shallow ground disturbance beneath vegetation based on images acquired by the NERC Airborne Thematic Mapper (ATM) at thermal infrared wavelengths. Shallow ground disturbance creates a differential heat flux due to a variation in the thermal properties between disturbed and undisturbed soils. When observed above a canopy, the effect of vegetation growth on the thermal regime of the underlying soils is poorly understood. The research extends current understanding by examining areas where ground disturbance is known to exist under variable vegetation cover at an archaeological site at Bosworth, Leicestershire and areas of abandoned mine activity on Baildon Moor, W. Yorkshire and in the N. Pennine Orefield, Weardale. The investigation focuses on qualitative image interpretation techniques, where anomalies on day and night thermal images are compared with those manifest on the multispectral images, and a more quantitative approach of Apparent Thermal Inertia (ATI) modelling. Physical thermal inertia is a parameter that is sensitive to volumetric variations in the soil, but cannot be measured directly using remote sensing techniques. However, an apparent thermal inertia is determined by examining the day and night temperature contrast of the surface, where spatial variations can signify potential features buried in the near-surface environment. Ground temperature profiling at the Bosworth site indicates that diurnal heat dissipates between 0.20-0.50m at an early stage in vegetation development with progressively lower diurnal amplitudes observed at 0.20m as the vegetation develops. Results also show that the time of diurnal maximum temperature occurs progressively later as vegetation develops, implying an importance for thermal image acquisition. The quantitative investigation concentrates on the Bosworth site where extensive ground geophysical prospection was performed and vertical soil samples extracted across features of variable multispectral, thermal and ATI response to enable comparison of the observed airborne thermal response with physical soil properties. Results suggest that there is a high correlation between ATI and soil moisture properties at 0.15-0.25m depth (R(^2)=0.99) at an early stage in cereal crop development but has a high correlation at a wider depth range (0.10-0.30m) at a later stage in development (R(^2)=0.98). The high correlation between physical ground disturbance and the thermal response is also corroborated qualitatively with the results of the resistivity surveys. The ATI modelling reveals similar features to those evident on day or night thermal images at an early stage in vegetation growth, suggesting that thermal imaging during the day at an early stage in vegetation growth may supply sufficient information on features buried in the near-surface environment. Airborne thermal imaging therefore provides a useful complementary prospection tool for archaeological and geological applications for surfaces covered by vegetation

Factors controlling seasonal succession of the copepods \u3cem\u3eAcartia hudsonica\u3c/em\u3e and \u3cem\u3eA. tonsa\u3c/em\u3e in Narragansett Bay, Rhode Island: temperature and resting egg production

We present evidence to show that the timing of the seasonal appearance and disappearance of Acartia hudsonica, the dominant winter-spring copepod in Narragansett Bay, a north temperate estuary, is controlled by temperature and its effect on reproductive rate and formation and hatching of resting eggs. Maximum reproductive rates and growth efficiency for this species were observed at temperatures below those typical of the mid-summer season when it is replaced by Acartia tonsa, the summer dominant. Furthermore, during early summer A. hudsonica produces eggs that do not hatch at the temperatures at which they are produced (\u3e 16 °C) and that will hatch only after exposure to low temperature. These eggs were also present in the sediments of Narragansett Bay and are probably true diapause eggs. It also appears that competition for food is not an important factor controlling seasonal succession of the species. Populations of both Acartia species were observed in 13 m3 enclosed ecosystems which differed from Narragansett Bay in that food supply was increased by addition of nutrients. Timing of the seasonal transition between A. hudsonica and A. tonsa was not altered in any consistent way by these changes, although population size increased in some years

CRISPR/Cas-based screening of long non-coding RNAs (lncRNAs) in macrophages with an NF-κB reporter.

The innate immune system protects against infections by initiating an inducible inflammatory response. NF-κB is one of the critical transcription factors controlling this complex response, but some aspects of its regulation remain unclear. For example, although long non-coding RNAs (lncRNAs) have been shown to critically regulate gene expression, only a fraction of these have been functionally characterized, and the extent to which lncRNAs control NF-κB expression is unknown. Here, we describe the generation of a GFP-based NF-κB reporter system in immortalized murine bone marrow-derived macrophages (iBMDM). Activation of this reporter, using Toll-like receptor ligands, resulted in GFP expression, which could be monitored by flow cytometry. We also established a CRISPR/Cas9 gene deletion system in this NF-κB reporter line, enabling us to screen for genes that regulate NF-κB signaling. Our deletion-based approach identified two long intergenic non-coding(linc)RNAs, lincRNA-Cox2 and lincRNA-AK170409, that control NF-κB signaling. We demonstrate a potential novel role for lincRNA-Cox2 in promoting IκBα degradation in the cytoplasm. For lincRNA-AK170409, we provide evidence that this nuclearly-localized lincRNA regulates a number of inflammation-related genes. In conclusion, we have established an NF-κB-GFP iBMDM reporter cell line and a line that stably expresses Cas9. Our approach enabled the identification of lincRNA-Cox2 and lincRNA-AK170409 as NF-κB regulators, and this tool will be useful for identifying additional genes involved in regulating this transcription factor critical for immune function

'We don't have any of those people here...'

Most people ageing with HIV in Australia are, and will continue to be, gay men. For those who avoided disclosing their sexuality throughout their lives or who have limited disclosure to a small circle, the prospect of dealing with aged-care services can be daunting. For many older gay men diagnosed with HIV in the eighties or nineties, the concerns around disclosing sexuality are compounded by past experiences of stigma and discrimination due to their sexuality, with additional fears around disclosure of their HIV-positive status. The GRAI research outlined in this article raises important issues that must be addressed in planning for the diversity of the Australian population - planning that needs to acknowledge the issues faced by the Australian cohort of gay men ageing with HIV. (Eds.

Association of the SULT1A1 R213H polymorphism with colorectal cancer

1. Sulphotransferases are a superfamily of enzymes involved in both detoxification and bioactivation of endogenous and exogenous compounds. The arylsulphotransferase SULT1A1 has been implicated in a decreased activity and thermostability when the wild-type arginine at position 213 of the coding sequence is substituted by a histidine. SULT1A1 is the isoform primarily associated with the conversion of dietary N -OH arylamines to DNA binding adducts and is therefore of interest to determine whether this polymorphism is linked to colorectal cancer. 2. Genotyping, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, was performed using DNA samples of healthy control subjects (n = 402) and patients with histologically proven colorectal cancer (n = 383). Both control and test populations possessed similar frequencies for the mutant allele (32.1 and 31%, respectively; P = 0.935). Results were not altered when age and gender were considered as potential confounders in a logistic regression analysis. 3. Examination of the sulphonating ability of the two allozymes with respect to the substrates p -nitrophenol and paracetamol showed that the affinity and rate of sulphonation was unaffected by substitution of arginine to histidine at position 213 of the amino acid sequence. 4. From this study, we conclude that the SULT1A1 R213H polymorphism is not linked with colorectal cancer in this elderly Australian population

The impact of blood donation deferral strategies on the eligibility of men who have sex with men and other sexual risk behavior in Australia

Background In Australia, a man cannot donate blood if he has had sex with another man within the past 3 months. However, this policy has been criticized as being discriminatory as it does not consider lower risk subgroups, and led to calls for modifications to the policy that more accurately distinguish risk among gay, bisexual, and other men who have sex with men (GBM). Study Design and Methods We used data from a nationally representative survey to estimate the proportion of GBM aged 18–74 years old who would be eligible to donate under current criteria and other scenarios. Results Among the 5178 survey participants, 155 (3.0%) were classified as GBM based on survey responses, Among the GBM, 40.2% (95% CI 28.0%–53.7%) were eligible to donate based on current criteria, and 21.0% (95% CI 14.5%–29.5%) were ineligible due to the 3 months deferral alone. Eligibility among GBM, all men, and the population increased as criteria were removed. Under the new Australian plasma donation criteria, 73.6% (95% CI 64.4%–81.1%) of GBM, 68.4% (95% CI 65.5%–71.2%) of all men, and 60.8% (95% CI 58.8%–62.8%) of the full population were estimated to be eligible. Only 16.1% (95% CI 8.6%–28.1%) of GBM knew that the male-to-male sex deferral period is 3 months. Discussion Changing the deferral criteria and sexual risk evaluation would lead to a higher proportion of GBM being eligible to donate blood. Knowledge of the current GBM deferral period is very low. Improved education about the current criteria and any future changes are required to improve blood donation rates

The re-birth of the "beat": A hyperlocal online newsgathering model

This is an Author's Accepted Manuscript of an article published in Journalism Practice, 6(5-6), 754 - 765, 2012, copyright Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/17512786.2012.667279.Scholars have long lamented the death of the 'beat' in news journalism. Today's journalists generate more copy than they used to, a deluge of PR releases often keeping them in the office, and away from their communities. Consolidation in industry has dislodged some journalists from their local sources. Yet hyperlocal online activity is thriving if journalists have the time and inclination to engage with it. This paper proposes an exploratory, normative schema intended to help local journalists systematically map and monitor their own hyperlocal online communities and contacts, with the aim of re-establishing local news beats online as networks. This model is, in part, technologically-independent. It encompasses proactive and reactive news-gathering and forward planning approaches. A schema is proposed, developed upon suggested news-gathering frameworks from the literature. These experiences were distilled into an iterative, replicable schema for local journalism. This model was then used to map out two real-world 'beats' for local news-gathering. Journalists working within these local beats were invited to trial the models created. It is hoped that this research will empower journalists by improving their information auditing, and could help re-define journalists' relationship with their online audiences

Serological evidence for human cystic echinococcosis in Slovenia

<p>Abstract</p> <p>Background</p> <p>Cystic echinococcosis (CE) is caused by the larva of tapeworm <it>Echinococcus granulosus</it>. Dogs and other canids are the primary definitive hosts for this parasite. CE may develop after accidental ingestion of tapeworm eggs, excreted with the feces of these animals. In the intestine, the larvae released from the eggs are nested in the liver, lungs or other organs of livestock as intermediate hosts and humans as aberrant hosts. The aim of this study was to examine serologically whether some of the patients in Slovenia, suspected of CE by imaging findings in the liver or lungs had been infected with the larva of <it>Echinococcus granulosus</it>.</p> <p>Methods</p> <p>Between January 1, 2002 and the end of December 2006, 1323 patients suspected of having echinococcosis were screened serologically by indirect haemagglutination assay (IHA). For confirmation and differentiation of <it>Echinococcus </it>spp. infection, the sera of IHA-positive patients were then retested by western blot (WB).</p> <p>Results</p> <p>Out of 127 IHA-positive sera, 34 sera were confirmed by WB and considered specific for CE. Of 34 sera of CE-positive patients sera, 32 corresponded to the characteristic imaging findings of a liver cysts and 2 to those of lung cysts. The mean age of CE-positive patients was 58.3 years. No significant differences were found between the CE-positive patients in regard to their sex.</p> <p>Conclusion</p> <p>In the study, it was found out that CE was mostly spread in the same area of Slovenia as in the past, but its prevalence decreased from 4.8 per 10⁵inhabitants in the period 1956–1968 to 1.7 per 10⁵inhabitants in the period 2002–2006. In spite of the decreased prevalence of CE in the last years, it is suggested that clinicians and public health authorities, especially in the eastern parts of Slovenia where the most CE patients come from, should pay greater attention to this disease in the future.</p

Epstein-barr virus latent membrane protein 1 genetic variability in peripheral blood B cells and oropharyngeal fluids

We report the diversity of latent membrane protein 1 (LMP1) gene founder sequences and the level of Epstein-Barr virus (EBV) genome variability over time and across anatomic compartments by using virus genomes amplified directly from oropharyngeal wash specimens and peripheral blood B cells during acute infection and convalescence. The intrahost nucleotide variability of the founder virus was 0.02% across the region sequences, and diversity increased significantly over time in the oropharyngeal compartment (P = 0.004). The LMP1 region showing the greatest level of variability in both compartments, and over time, was concentrated within the functional carboxyl-terminal activating regions 2 and 3 (CTAR2 and CTAR3). Interestingly, a deletion in a proline-rich repeat region (amino acids 274 to 289) of EBV commonly reported in EBV sequenced from cancer specimens was not observed in acute infectious mononucleosis (AIM) patients. Taken together, these data highlight the diversity in circulating EBV genomes and its potential importance in disease pathogenesis and vaccine design. IMPORTANCE: This study is among the first to leverage an improved high-throughput deep-sequencing methodology to investigate directly from patient samples the degree of diversity in Epstein-Barr virus (EBV) populations and the extent to which viral genome diversity develops over time in the infected host. Significant variability of circulating EBV latent membrane protein 1 (LMP1) gene sequences was observed between cellular and oral wash samples, and this variability increased over time in oral wash samples. The significance of EBV genetic diversity in transmission and disease pathogenesis are discussed

Characterisation of the Immunophenotype of Dogs with Primary Immune-Mediated Haemolytic Anaemia

Immune-mediated haemolytic anaemia (IMHA) is reported to be the most common autoimmune disease of dogs, resulting in significant morbidity and mortality in affected animals. Haemolysis is caused by the action of autoantibodies, but the immunological changes that result in their production have not been elucidated.To investigate the frequency of regulatory T cells (Tregs) and other lymphocyte subsets and to measure serum concentrations of cytokines and peripheral blood mononuclear cell expression of cytokine genes in dogs with IMHA, healthy dogs and dogs with inflammatory diseases.19 dogs with primary IMHA, 22 dogs with inflammatory diseases and 32 healthy control dogs.Residual EDTA-anti-coagulated blood samples were stained with fluorophore-conjugated monoclonal antibodies and analysed by flow cytometry to identify Tregs and other lymphocyte subsets. Total RNA was also extracted from peripheral blood mononuclear cells to investigate cytokine gene expression, and concentrations of serum cytokines (interleukins 2, 6 10, CXCL-8 and tumour necrosis factor α) were measured using enhanced chemiluminescent assays. Principal component analysis was used to investigate latent variables that might explain variability in the entire dataset.There was no difference in the frequency or absolute numbers of Tregs among groups, nor in the proportions of other lymphocyte subsets. The concentrations of pro-inflammatory cytokines were greater in dogs with IMHA compared to healthy controls, but the concentration of IL-10 and the expression of cytokine genes did not differ between groups. Principal component analysis identified four components that explained the majority of the variability in the dataset, which seemed to correspond to different aspects of the immune response.The immunophenotype of dogs with IMHA differed from that of dogs with inflammatory diseases and from healthy control dogs; some of these changes could suggest abnormalities in peripheral tolerance that permit development of autoimmune disease. The frequency of Tregs did not differ between groups, suggesting that deficiency in the number of these cells is not responsible for development of IMHA