Data Analysis with PLSR models

Land condition monitoring information is required for the strategic management of grazing land and for a better understanding of ecosystem processes. Yet, for policy makers and those land managers whose properties are situated within north-eastern Australia's vast Great Barrier Reef catchments, there has been a general lack of geospatial land condition monitoring information. This paper provides an overview of integrated land monitoring activity in rangeland areas of two major Reef catchments in Queensland: the Burdekin and Fitzroy regions. The project aims were to assemble land condition monitoring datasets that would assist grazing land management and support decision-makers investing public funds; and deliver these data to natural resource management(NRM) community groups, which had been given increased responsibility for delivering local environmental outcomes. We describe the rationale and processes used to produce new land condition monitoring datasets derived from remotely sensed Landsat thematic mapper (TM) and high resolution SPOT 5 satellite imagery and from rapid land condition ground assessment. Specific products include subcatchment groundcover change maps, regional mapping of indicative very poor land condition, and stratified land condition site summaries. Their application, integration, and limitations are discussed. The major innovation is a better understanding of NRM issues with respect to land condition across vast regional areas, and the effective transfer of decision-making capacity to the local level. Likewise, with an increased ability to address policy questions from an evidence-based position, combined with increased cooperation between community, industry and all levels of government, a new era has emerged for decision-makers in rangeland management

The role of integrated information acquisition and management in the analysis of coastal ecosystem change

This book chapter represents a synthesis of the work which started in my PhD and which has been the conceptual basis for all of my research since 1993. The chapter presents a method for scientists and managers to use for selecting the type of remotely sensed data to use to meet their information needs associated with a mapping, monitoring or modelling application. The work draws on results from several of my ARC projects, CRC Rainforest and Coastal projects and theses of P.Scarth , K.Joyce and C.Roelfsema

Global warming and mass extinctions associated with large igneous province volcanism

The coincidence of large igneous province (LIP) eruptions with at least three, if not all of the “Big Five” biotic crises of the Phanerozoic implies that volcanism is a key driver of mass extinctions. Many LIP-induced extinction scenarios invoke global warming, caused primarily (but not exclusively) by greenhouse gases emitted at the site of LIP emplacement and by contact metamorphism of carbon-rich host rocks. Here we explore a) the climate-changing products of volcanism including sulfur dioxide (SO2), carbon dioxide (CO2) and methane (CH4) from eruptions, contact metamorphism, and melting (dissociation) of gas hydrates; b) their deadly effects, including marine anoxia and thermal stress; c) increasingly sophisticated paleotemperature proxies (e.g. δ18O of shell material) through case studies of the best-known LIP-warming-extinction nexi; and d) global warming through the lens of the putative “Anthropocene” extinction

Clinical outcome following acute ischaemic stroke relates to both activation and autoregulatory inhibition of cytokine production

BACKGROUND: As critical mediators of local and systemic inflammatory responses, cytokines are produced in the brain following ischaemic stroke. Some have been detected in the circulation of stroke patients, but their role and source is unclear. Focusing primarily on interleukin(IL)-1-related mechanisms, we serially measured plasma inflammatory markers, and the production of cytokines by whole blood, from 36 patients recruited within 12 h and followed up to 1 year after acute ischaemic stroke (AIS). RESULTS: Admission plasma IL-1 receptor antagonist (IL-1ra) concentration was elevated, relative to age-, sex-, and atherosclerosis-matched controls. IL-1β, soluble IL-1 receptor type II, tumour necrosis factor (TNF)-α, TNF-RII, IL-10 and leptin concentrations did not significantly differ from controls, but peak soluble TNF receptor type I (sTNF-RI) in the first week correlated strongly with computed tomography infarct volume at 5–7 days, mRS and BI at 3 and 12 months. Neopterin was raised in patients at 5–7 d, relative to controls, and in subjects with significant atherosclerosis. Spontaneous IL-1β, TNF-α and IL-6 gene and protein expression by blood cells was minimal, and induction of these cytokines by lipopolysaccharide (LPS) was significantly lower in patients than in controls during the first week. Minimum LPS-induced cytokine production correlated strongly with mRS and BI, and also with plasma cortisol. CONCLUSION: Absence of spontaneous whole blood gene activation or cytokine production suggests that peripheral blood cells are not the source of cytokines measured in plasma after AIS. Increased plasma IL-1ra within 12 h of AIS onset, the relationship between sTNF-RI and stroke severity, and suppressed cytokine induction suggests early activation of endogenous immunosuppressive mechanisms after AIS

Cancer risks associated with germline PALB2 pathogenic variants: An international study of 524 families

PURPOSE To estimate age-specific relative and absolute cancer risks of breast cancer and to estimate risks of ovarian, pancreatic, male breast, prostate, and colorectal cancers associated with germline PALB2 pathogenic variants (PVs) because these risks have not been extensively characterized. METHODS We analyzed data from 524 families with PALB2 PVs from 21 countries. Complex segregation analysis was used to estimate relative risks (RRs; relative to country-specific population incidences) and absolute risks of cancers. The models allowed for residual familial aggregation of breast and ovarian cancer and were adjusted for the family-specific ascertainment schemes. RESULTS We found associations between PALB2 PVs and risk of female breast cancer (RR, 7.18; 95% CI, 5.82 to 8.85; P = 6.5 × 10-76), ovarian cancer (RR, 2.91; 95% CI, 1.40 to 6.04; P = 4.1 × 10-3), pancreatic cancer (RR, 2.37; 95% CI, 1.24 to 4.50; P = 8.7 × 10-3), and male breast cancer (RR, 7.34; 95% CI, 1.28 to 42.18; P = 2.6 3 1022). There was no evidence for increased risks of prostate or colorectal cancer. The breast cancer RRs declined with age (P for trend = 2.0 × 10-3). After adjusting for family ascertainment, breast cancer risk estimates on the basis of multiple case families were similar to the estimates from families ascertained through population-based studies (P for difference = .41). On the basis of the combined data, the estimated risks to age 80 years were 53% (95% CI, 44% to 63%) for female breast cancer, 5% (95% CI, 2% to 10%) for ovarian cancer, 2%-3% (95% CI females, 1% to 4%; 95% CI males, 2% to 5%) for pancreatic cancer, and 1% (95% CI, 0.2% to 5%) for male breast cancer. CONCLUSION These results confirm PALB2 as a major breast cancer susceptibility gene and establish substantial associations between germline PALB2 PVs and ovarian, pancreatic, and male breast cancers. These findings will facilitate incorporation of PALB2 into risk prediction models and optimize the clinical cancer risk management of PALB2 PV carriers

The Relationship between Dioxin-Like Polychlorobiphenyls and IGF-I Serum Levels in Healthy Adults: Evidence from a Cross-Sectional Study

OBJECTIVE: Insulin-like growth factor I (IGF-I) and dioxin-like polychlorobiphenyls (DL-PCBs) have been associated with the pathogenesis of several diseases like cancer, diabetes and growth disorders. Because it has been suggested that organohalogenated contaminants could influence IGF-I levels in adults, the potential relationship between DL-PCBs and IGF-I serum levels was studied in 456 healthy adults from a representative sample of the general population of the Canary Islands (Spain). DESIGN: Free circulating serum levels of IGF-I and IGFBP-3 were measured through an ELISA methodology, while the serum levels of the 12 DL-PCBs congeners (IUPAC numbers # 77, 81, 105, 114, 118, 123, 126, 156, 157, 167, 169, and 189) were measured by gas chromatography/mass spectrometry (GC-MS). RESULTS: DL-PCBs 156 and 167, Total DL-PCBs body burden (∑PCBs: sum over the 12 measured DL-PCBs), and Total toxic burden (in terms of toxic equivalence to dioxins: ∑TEQs) showed a trend of inverse association with IGF-I serum levels in the whole studied population. After adjusting for potential confounders, including gender, body mass index (BMI), age, and IGF-binding protein-3 (IGFBP-3), younger (18-45 years) women with lower BMI (<27 kg/m(2)) and detectable levels of DL-PCB-156 showed significantly lower IGF-I levels than those in the same age and BMI subgroup with non-detectable levels of DL-PCB-156 (p<0.001). Similarly, ∑PCBs and ∑TEQs showed a tendency to an inverse association with IGF-I levels in the same group of women (p=0.017 and p=0.019 respectively). CONCLUSIONS: These findings suggest that DL-PCBs could be involved in the regulation of the IGF-system in a way possibly influenced by gender, age and BMI. Although these results should be interpreted with caution, such circumstances could contribute to explain the development of diseases associated to the IGF system

Fractional vegetation cover of East African wetlands observed on ground and from space

Wetlands are important ecosystems providing numerous ecosystem services. They are of particular importance to communities in East Africa where agriculture is the most important economic sector and where food availability to households critical. During an intensive field campaign in the dry season of 2013 were Fractional Vegetation Cover (FVC) measurements, botanical vegetation cover and vegetation structure estimates acquired in three wetland test sites within the East African region. FVC cover data were collated in three strata: ground layer, midstorey and overstorey (woody vegetation greater than 2 m). Fractional cover estimates for the green and no-green vegetative fraction were calculated for Landsat MODIS imagery. These FVC data products were evaluated a) with FVC field data and b) relative to each other for their usability in the East African region. First results show some promise for further studies