Reconstructing paleoseismic deformation, 2: 1000 years of great earthquakes at Chucalén, south central Chile

In this paper we adopt a quantitative biostratigraphic approach to establish a 1000-year-long coastal record of megathrust earthquake and tsunami occurrence in south central Chile. Our investigations focus on a site in the centre of the rupture segment of the largest instrumentally recorded earthquake, the AD 1960 magnitude 9.5 Chile earthquake. At Chucalén coseismic subsidence in 1960 is recorded in the lithostratigraphy and biostratigraphy of coastal marshes, with peat overlain by minerogenic sediment and changes in the assemblages of diatoms (unicellular algae) indicating an abrupt increase in relative sea level. In addition to the 1960 earthquake, the stratigraphy at Chucalén records three earlier earthquakes, the historically documented earthquake of 1575 and two prehistoric earthquakes, radiocarbon dated to AD 1270–1450 and 1070–1220. Laterally extensive sand sheets containing marine or brackish diatom assemblages suggest tsunami deposition associated with at least two of the three pre-1960 earthquakes. The record presented here suggests a longer earthquake recurrence interval, averaging 270 years, than the historical recurrence interval, which averages 128 years. The lack of geologic evidence at Chucalén of two historically documented earthquakes, in 1737 and 1837, supports the previously suggested hypothesis of variability in historical earthquake characteristics. Our estimates of coseismic land-level change for the four earthquakes range from meter-scale subsidence to no subsidence or slight uplift, suggesting earthquakes completing each ∼270 year cycle may not share a common, characteristic slip distribution. The presence of buried soils at elevations below their modern equivalents implies net relative sea-level rise over the course of the Chucalén paleoseismic record, in contrast to relative sea-level fall over preceding millennia inferred from sites on the mainland. Sea-level rise may contribute to the preservation of evidence for multiple earthquakes during the last millennium, while net relative sea-level fall over the last 2000–5000 years may explain the lack of evidence for older earthquakes

The Mining and Analysis of Data with Mixed Attribute Types

Ed Wakelam, Neil Davey, Yi Sun, Amanda Jefferies, Parimala Alva, and Alex Hocking, ‘The Mining and Analysis of Data with Mixed Attribute Types’, paper presented at the IMMM 2016: Sixth International Conference on Advances in Information Mining and Management, 22 May 2016 – 26 May 2016, Valencia, Spain. Published by IARIA XPS Press, Archived in the free access ThinkMind™ Digital Library. Available online at http://www.thinkmind.org/index.php?view=article&articleid=immm_2016_3_20_50067 © IARIA, 2016Mining and analysis of large data sets has become a major contributor to the exploitation of Artificial Intelligence in a wide range of real life challenges, including education, business intelligence and research. In the field of education, the mining, extraction and exploitation of useful information and patterns from student data provides lecturers, trainers and organisations with the potential to tailor learning paths and materials to maximize teaching efficiency and to predict and influence student success rates. Progress in this important area of student data analytics can provide useful techniques for exploitation in the development of adaptive learning systems. Student data often includes a combination of nominal and numeric data. A large variety of techniques are available to analyse numeric data, however there are fewer techniques applicable to nominal data. In this paper, we summarise our progress in applying a combination of what we believe to be a novel technique to analyse nominal data by making a systematic comparison of data pairs, followed by numeric data analysis, providing the opportunity to focus on promising correlations for deeper analysis.Final Accepted Versio

Geological evidence of an unreported historical Chilean tsunami reveals more frequent inundation

Assessing tsunami hazards commonly relies on historical accounts of past inundations, but such chronicles may be biased by temporal gaps due to historical circumstances. As a possible example, the lack of reports of tsunami inundation from the 1737 south-central Chile earthquake has been attributed to either civil unrest or a small tsunami due to deep fault slip below land. Here we conduct sedimentological and diatom analyses of tidal marsh sediments within the 1737 rupture area and find evidence for a locally-sourced tsunami consistent in age with this event. The evidence is a laterally-extensive sand sheet coincident with abrupt, decimetric subsidence. Coupled dislocation-tsunami models place the causative fault slip mostly offshore rather than below land. Whether associated or not with the 1737 earthquake, our findings reduce the average recurrence interval of tsunami inundation derived from historical records alone, highlighting the importance of combining geological and historical records in tsunami hazard assessment

A new look at the LTR retrotransposon content of the chicken genome

BACKGROUND: LTR retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds. A novel LTR retrotransposon classification pipeline, LocaTR, was developed and subsequently utilised to re-examine the chicken LTR retrotransposon annotation, and determine if the proposed chicken deficit is biologically accurate or simply a technical artefact. RESULTS: Using LocaTR 3.01 % of the chicken galGal4 genome assembly was annotated as LTR retrotransposon-derived elements (nearly double the previous annotation), including 1,073 that were structurally intact. Element distribution is significantly correlated with chromosome size and is non-random within each chromosome. Elements are significantly depleted within coding regions and enriched in gene sparse areas of the genome. Over 40 % of intact elements are found in clusters, unrelated by age or genera, generally in poorly recombining regions. The transcription of most LTR retrotransposons were suppressed or incomplete, but individual domain and full length retroviral transcripts were produced in some cases, although mostly with regularly interspersed stop codons in all reading frames. Furthermore, RNAseq data from 23 diverse tissues enabled greater characterisation of the co-opted endogenous retrovirus Ovex1. This gene was shown to be expressed ubiquitously but at variable levels across different tissues. LTR retrotransposon content was found to be very variable across the avian lineage and did not correlate with either genome size or phylogenetic position. However, the extent of previous, species-specific LTR retrotransposon annotation appears to be a confounding factor. CONCLUSIONS: Use of the novel LocaTR pipeline has nearly doubled the annotated LTR retrotransposon content of the chicken genome compared to previous estimates. Further analysis has described element distribution, clustering patterns and degree of expression in a variety of adult tissues, as well as in three embryonic stages. This study also enabled better characterisation of the co-opted gamma retroviral envelope gene Ovex1. Additionally, this work suggests that there is no deficit of LTR retrotransposons within the Galliformes relative to other birds, or to mammalian genomes when scaled for the three-fold difference in genome size

Simulating long-term carbon nitrogen and phosphorus biogeochemical cycling in agricultural environments

Understanding how agricultural practices alter biogeochemical cycles is vital for maintaining land productivity, food security, and other ecosystem services such as carbon sequestration. However, these are complex, highly coupled long-term processes that are difficult to observe or explore through empirical science alone. Models are required that capture the main anthropogenic disturbances, whilst operating across regions and long timescales, simulating both natural and agricultural environments, and shifts among these. Many biogeochemical models neglect agriculture or interactions between carbon and nutrient cycles, which is surprising given the scale of intervention in nitrogen and phosphorus cycles introduced by agriculture. This gap is addressed here, using a plant-soil model that simulates integrated soil carbon, nitrogen and phosphorus (CNP) cycling across natural, semi-natural and agricultural environments. The model is rigorously tested both spatially and temporally using data from long-term agricultural experiments across temperate environments. The model proved capable of reproducing the magnitude of and trends in soil nutrient stocks, and yield responses to nutrient addition. The model has potential to simulate anthropogenic effects on biogeochemical cycles across northern Europe, for long timescales (centuries) without site-specific calibration, using easily accessible input data. The results demonstrate that weatherable P from parent material has a considerable effect on modern pools of soil C and N, despite significant perturbation of nutrient cycling from agricultural practices, highlighting the need to integrate both geological and agricultural processes to understand effects of land-use change on food security, C storage and nutrient sustainability. The results suggest that an important process or source of P is currently missing in our understanding of agricultural biogeochemical cycles. The model could not explain how yields were sustained in plots with low P fertiliser addition. We suggest that plant access to organic P is a key uncertainty warranting further research, particularly given sustainability concerns surrounding rock sources of P fertiliser

Lack of Chemokine Signaling through CXCR5 Causes Increased Mortality, Ventricular Dilatation and Deranged Matrix during Cardiac Pressure Overload

RATIONALE: Inflammatory mechanisms have been suggested to play a role in the development of heart failure (HF), but a role for chemokines is largely unknown. Based on their role in inflammation and matrix remodeling in other tissues, we hypothesized that CXCL13 and CXCR5 could be involved in cardiac remodeling during HF. OBJECTIVE: We sought to analyze the role of the chemokine CXCL13 and its receptor CXCR5 in cardiac pathophysiology leading to HF. METHODS AND RESULTS: Mice harboring a systemic knockout of the CXCR5 (CXCR5(-/-)) displayed increased mortality during a follow-up of 80 days after aortic banding (AB). Following three weeks of AB, CXCR5(-/-) developed significant left ventricular (LV) dilatation compared to wild type (WT) mice. Microarray analysis revealed altered expression of several small leucine-rich proteoglycans (SLRPs) that bind to collagen and modulate fibril assembly. Protein levels of fibromodulin, decorin and lumican (all SLRPs) were significantly reduced in AB CXCR5(-/-) compared to AB WT mice. Electron microscopy revealed loosely packed extracellular matrix with individual collagen fibers and small networks of proteoglycans in AB CXCR5(-/-) mice. Addition of CXCL13 to cultured cardiac fibroblasts enhanced the expression of SLRPs. In patients with HF, we observed increased myocardial levels of CXCR5 and SLRPs, which was reversed following LV assist device treatment. CONCLUSIONS: Lack of CXCR5 leads to LV dilatation and increased mortality during pressure overload, possibly via lack of an increase in SLRPs. This study demonstrates a critical role of the chemokine CXCL13 and CXCR5 in survival and maintaining of cardiac structure upon pressure overload, by regulating proteoglycans essential for correct collagen assembly

Functional Genomics Unique to Week 20 Post Wounding in the Deep Cone/Fat Dome of the Duroc/Yorkshire Porcine Model of Fibroproliferative Scarring

Background: Hypertrophic scar was first described over 100 years ago; PubMed has more than 1,000 references on the topic. Nevertheless prevention and treatment remains poor, because 1) there has been no validated animal model; 2) human scar tissue, which is impossible to obtain in a controlled manner, has been the only source for study; 3) tissues typically have been homogenized, mixing cell populations; and 4) gene-by-gene studies are incomplete.Methodology/Principal Findings: We have assembled a system that overcomes these barriers and permits the study of genome-wide gene expression in microanatomical locations, in shallow and deep partial-thickness wounds, and pigmented and non-pigmented skin, using the Duroc( pigmented fibroproliferative)/Yorkshire( non-pigmented non-fibroproliferative) porcine model. We used this system to obtain the differential transcriptome at 1, 2, 3, 12 and 20 weeks post wounding. It is not clear when fibroproliferation begins, but it is fully developed in humans and the Duroc breed at 20 weeks. Therefore we obtained the derivative functional genomics unique to 20 weeks post wounding. We also obtained long-term, forty-six week follow-up with the model.Conclusions/Significance: 1) the scars are still thick at forty-six weeks post wounding further validating the model. 2) the differential transcriptome provides new insights into the fibroproliferative process as several genes thought fundamental to fibroproliferation are absent and others differentially expressed are newly implicated. 3) the findings in the derivative functional genomics support old concepts, which further validates the model, and suggests new avenues for reductionist exploration. in the future, these findings will be searched for directed networks likely involved in cutaneous fibroproliferation. These clues may lead to a better understanding of the systems biology of cutaneous fibroproliferation, and ultimately prevention and treatment of hypertrophic scarring.The National Institute on Disability and Rehabilitation ResearchThe National Institutes of HealthThe Washington State Council of Fire Fighters Burn FoundationThe Northwest Burn FoundationUniv Washington, Dept Surg, Div Plast Surg, Seattle, WA 98195 USAIowa State Univ, Dept Anim Sci, Ames, IA USAUniv Washington, Dept Biostat, Seattle, WA 98195 USAMahidol Univ, Ramathibodi Hosp, Dept Surg, Bangkok 10700, ThailandUniv Washington, Dept Environm & Occupat Hlth Sci, Seattle, WA 98195 USAUniversidade Federal de São Paulo, Div Plast Surg, Dept Surg, São Paulo, BrazilUniversidade Federal de São Paulo, Div Plast Surg, Dept Surg, São Paulo, BrazilThe National Institute on Disability and Rehabilitation Research: H133G050022The National Institutes of Health: 1R21GM074673The National Institutes of Health: 5U54GM062119-09Web of Scienc

Ethnic differences in the association between depression and chronic pain:cross sectional results from UK Biobank

<b>Background</b> Comorbid chronic pain and depression is a challenging dyad of conditions to manage in primary care and reporting has shown to vary by ethnic group. Whether the relationship between depression and chronic pain varies by ethnicity is unclear. This study aims to explore chronic pain and depression reporting across ethnic groups and examine whether this association differs, independently of potential confounding factors. <p></p> <b>Methods</b> Cross-sectional study of UK Biobank participants with complete data on chronic pain and probable lifetime history of depression, who reported their ethnic group as White, Asian/Asian British or Black/Black British. Chronic pain classification: present if participants had ≥ 1 site of body pain (up to seven sites or “pain all over the body” could be selected) that lasted ≥ 3 months; extent of chronic pain categories: 0, 1, 2–3, 4–7 sites or pain all over the body. Probable depression classification: an algorithm of low mood, anhedonia and help-seeking behaviour. Relationship between depression and presence/extent of chronic pain assessed using logistic/multinomial regression models (odds ratio (OR); relative risk ratio (RRR), 95 % confidence intervals), adjusted for sociodemographic, lifestyle, and morbidity factors; and a final adjustment for current depressive symptoms. <p></p> <b>Results</b> The number of participants eligible for inclusion was 144,139: 35,703 (94 %) White, 4539 (3 %) Asian, and 3897 (3 %) Black. Chronic pain was less (40.5 %, 45.8 %, 45.0 %, respectively) and depression more (22.1 %, 12.9 %, 13.8 %, respectively) commonly reported in White participants than Asian and Black participants. Statistically significant associations between depression and presence/extent of chronic pain persisted following adjustment for potential confounding variables; this relationship was strongest for Black participants (presence of chronic pain: OR 1.86 (1.52, 2.27); RRR 1 site 1.49 (1.16, 1.91), 2–3 sites 1.98 (1.53, 2.56), 4–7 sites 3.23 (2.09, 4.99), pain all over the body 3.31 (2.05, 5.33). When current depressive symptoms were considered these relationships were attenuated. <p></p> <b>Conclusions</b> Chronic pain and depression reporting varies across ethnic groups. Differences in health seeking behaviour between ethnic groups may impact on the results reported. Clinicians, particularly in primary care, need to be aware of the cultural barriers within certain ethic groups to expressing concern over mood and to consider their approach accordingly