Environmental signal propagation, preservation and shredding in sedimentary systems

Sediment flux is an important control on the morphology of sedimentary landscapes and stratigraphy as it sets the rates and scales of landscape dynamics. For example, sediment flux influences the shape and style of river channels, the avulsion frequency of rivers, and the position of shorelines. Over long timescales, the sediment flux through sediment routing systems relates to environmental forcing conditions such as climate and tectonics, which set rates of catchment erosion and sediment transport. This makes stratigraphy accumulating in sedimentary basins record a potential archive of past climatic and tectonic conditions that could inform our understanding of current and future environmental change. However, we may not always be able to identify environmental signals in the stratigraphic record because of stochastic processes in sedimentary systems (autogenics) that have the potential to obscure the transfer of environmental signals (allogenics) to landscapes and stratigraphy. Previous work demonstrates that autogenic landscape processes act as a low-pass filter on the transfer of environmental signals to the stratigraphic record, but signal amplitude must play a role too. A quantitative understanding of the conditions required to archive environmental signals is essential to underpin interpretations of these signals in the stratigraphic record. The aim of this thesis is to develop a quantitative theoretical basis that can be used to assess the stratigraphic record as an archive for allogenic signals of varying sediment flux. First, I present a new theoretical framework that predicts a time-dependent magnitude threshold for the transfer of allogenic sediment supply signals to the stratigraphic record. The minimum signal amplitude is set by autogenic processes and decreases as an exponential function of signal duration. This new framework is supported by physical delta experiments specifically designed to test the framework. The threshold was constructed using an experiment forced with constant sediment supply rate and tested with four new experiments with similar forcing conditions, but cyclic sediment flux. Signals with a combination of cycle magnitude and duration that exceed the threshold are transferred to the stratigraphic record, while signals that fall below the threshold are not. The threshold framework relies on high-resolution measurements of autogenic sediment fluxes, which are usually not available in stratigraphic studies. However, the exponential decay of the threshold can be approximated from long-term accumulation rates and an estimate of timescales at which autogenic processes level out. This approximation is applied to field-scale examples of the Pleistocene Kerinitis delta (Greece) and the Eocene Escanilla sediment routing system (Spain) to test whether Milankovitch-scale sediment supply cycles could realistically have been preserved in the stratigraphic record of these systems. The delta experiments were also used to study how sediment supply cycles of different magnitudes and durations influence delta morphodynamics. The stochastic variability of autogenic processes obscures most theoretical relationships between sediment flux and morphodynamic processes. However, the experiments demonstrate that signals with a high rate of sediment supply change (acceleration) are likely to push existing morphology out of equilibrium, and thereby generate cyclicity in landscape evolution. Slowly accelerating signals increase channel depth, but do not affect floodplain morphology or the number of co-existing channels, like quickly accelerating channels do. Quickly accelerating highfrequency signals, however, may not leave thick enough deposits to withstand erosion prior to permanent burial, and so their preservation potential is limited. The results of this thesis: (1) provide a theoretical framework that predicts the scales of sediment flux signals we may expect to find in the stratigraphic record; (2) detail how the threshold framework can be applied to the rock record, using datasets of limited temporal resolution; and (3) inform earth scientists of landscape response to sediment supply signals with different combinations of signal magnitude, duration and acceleration. As such, this work contributes to a more quantitative understanding of the effects of environmental signals on landscapes and the stratigraphic record

A Big Fan of Signals? Exploring Autogenic and Allogenic Process and Product In a Numerical Stratigraphic Forward Model of Submarine-Fan Development

Distinguishing an allogenic signal from trends and patterns produced by autogenic processes is a critical element in interpreting, understanding, and predicting strata. Lobyte3D is a new reduced-complexity model of dispersive flow over an evolving topography on fan systems that produces surprisingly complex potentially hierarchical strata despite a simple formulation. Two submarine-fan model scenarios are run, one with constant sediment input, and one with a sinusoidal variation in sediment input with an oscillation period of 25 ky and a peak-to-trough 80% volume change. Both model scenarios show that flows cluster to produce lobes which migrate and can rapidly switch location. Runs tests that can detect thickening and thinning bed trends and spectral analysis that detects the frequency of any signal present suggest that strata can be ordered even in the absence of any allogenic signal, with cycles and trends in bed thickness, but no single characteristic frequency. In the oscillating-supply scenario, an allogenic signal is present in places, particularly in the axial mid fan, but may be difficult to distinguish from the autogenic signal with only limited outcrop data, and without knowing a priori how the allogenic signal is likely to be preserved in complex and incomplete strata. Based on these limited model results we hypothesize that analysis of mid-fan vertical sections, using simple power-spectrum analysis and counting of the significant peaks present across a range of frequencies, may allow identification of a “signal bump” that could be evidence of the presence and nature of allocyclic forcing. Further Lobyte3D modeling work will explore if and how the “signal bump” is preserved with input signals across a range of frequencies and amplitudes, to guide further data collection and interpretation in outcrop and subsurface strata

Leg disorders in broiler chickens : prevalence, risk factors and prevention

Broiler (meat) chickens have been subjected to intense genetic selection. In the past 50 years, broiler growth rates have increased by over 300% (from 25 g per day to 100 g per day). There is growing societal concern that many broiler chickens have impaired locomotion or are even unable to walk. Here we present the results of a comprehensive survey of commercial flocks which quantifies the risk factors for poor locomotion in broiler chickens.We assessed the walking ability of 51,000 birds, representing 4.8 million birds within 176 flocks.We also obtained information on approximately 150 different management factors associated with each flock. At a mean age of 40 days, over 27.6% of birds in our study showed poor locomotion and 3.3% were almost unable to walk. The high prevalence of poor locomotion occurred despite culling policies designed to remove severely lame birds from flocks. We show that the primary risk factors associated with impaired locomotion and poor leg health are those specifically associated with rate of growth. Factors significantly associated with high gait score included the age of the bird (older birds), visit (second visit to same flock), bird genotype, not feeding whole wheat, a shorter dark period during the day, higher stocking density at the time of assessment, no use of antibiotic, and the use of intact feed pellets. The welfare implications are profound. Worldwide approximately 261010 broilers are reared within similar husbandry systems.We identify a range of management factors that could be altered to reduce leg health problems, but implementation of these changes would be likely to reduce growth rate and production. A debate on the sustainability of current practice in the production of this important food source is required

Development of high-throughput methods to screen disease caused by Rhizoctonia solani AG 2-1 in oilseed rape

Background: Rhizoctonia solani (Kühn) is a soil-borne, necrotrophic fungus causing damping off, root rot and stem canker in many cultivated plants worldwide. Oilseed rape (OSR, Brassica napus) is the primary host for anastomosis group (AG) 2-1 of R. solani causing pre- and post-emergence damping-off resulting in death of seedlings and impaired crop establishment. Presently, there are no known resistant OSR genotypes and the main methods for disease control are fungicide seed treatments and cultural practices. The identification of sources of resistance for crop breeding is essential for sustainable management of the disease. However, a high-throughput, reliable screening method for resistance traits is required. The aim of this work was to develop a low cost, rapid screening method for disease phenotyping and identification of resistance traits. Results: Four growth systems were developed and tested: (1) nutrient media plates, (2) compost trays, (3) light expanded clay aggregate (LECA) trays, and (4) a hydroponic pouch and wick system. Seedlings were inoculated with virulent AG 2-1 to cause damping-off disease and grown for a period of 4–10 days. Visual disease assessments were carried out or disease was estimated through image analysis using ImageJ. Conclusion: Inoculation of LECA was the most suitable method for phenotyping disease caused by R. solani AG 2-1 as it enabled the detection of differences in disease severity among OSR genotypes within a short time period whilst allowing measurements to be conducted on whole plants. This system is expected to facilitate identification of resistant germplasm

Field trial of three different Plasmodium vivax-detecting rapid diagnostic tests with and without evaporative cool box storage in Afghanistan

<p>Abstract</p> <p>Background</p> <p>Accurate parasitological diagnosis of malaria is essential for targeting treatment where more than one species coexist. In this study, three rapid diagnostic tests (RDTs) (AccessBio CareStart (CSPfPan), CareStart PfPv (CSPfPv) and Standard Diagnostics Bioline (SDBPfPv)) were evaluated for their ability to detect natural <it>Plasmodium vivax </it>infections in a basic clinic setting. The potential for locally made evaporative cooling boxes (ECB) to protect the tests from heat damage in high summer temperatures was also investigated.</p> <p>Methods</p> <p>Venous blood was drawn from <it>P. vivax </it>positive patients in Jalalabad, Afghanistan and tested against a panel of six RDTs. The panel comprised two of each test type; one group was stored at room temperature and the other in an ECB. RDT results were evaluated against a consensus gold standard based on two double-read reference slides and PCR. The sensitivity, specificity and a measure of global performance for each test were determined and stratified by parasitaemia level and storage condition.</p> <p>Results</p> <p>In total, 306 patients were recruited, of which 284 were positive for <it>P. vivax</it>, one for <it>Plasmodium malariae </it>and none for <it>Plasmodium falciparum</it>; 21 were negative. All three RDTs were specific for malaria. The sensitivity and global performance index for each test were as follows: CSPfPan [98.6%, 95.1%], CSPfPv [91.9%, 90.5%] and SDBPfPv [96.5%, 82.9%], respectively. CSPfPv was 16% less sensitive to a parasitaemia below 5,000/μL. Room temperature storage of SDBPfPv led to a high proportion of invalid results (17%), which reduced to 10% in the ECB. Throughout the testing period, the ECB maintained ~8°C reduction over ambient temperatures and never exceeded 30°C.</p> <p>Conclusions</p> <p>Of the three RDTs, the CSPfPan test was the most consistent and reliable, rendering it appropriate for this <it>P. vivax </it>predominant region. The CSPfPv test proved unsuitable owing to its reduced sensitivity at a parasitaemia below 5,000/μL (affecting 43% of study samples). Although the SDBPfPv device was more sensitive than the CSPfPv test, its invalid rate was unacceptably high. ECB storage reduced the proportion of invalid results for the SDBPfPv test, but surprisingly had no impact on RDT sensitivity at low parasitaemia.</p

Deployment of ACT antimalarials for treatment of malaria: challenges and opportunities

Following a long period when the effectiveness of existing mono-therapies for antimalarials was steadily declining with no clear alternative, most malaria-endemic countries in Africa and Asia have adopted artemisinin combination therapy (ACT) as antimalarial drug policy. Several ACT drugs exist and others are in the pipeline. If properly targeted, they have the potential to reduce mortality from malaria substantially. The major challenge now is to get the drugs to the right people. Current evidence suggests that most of those who need the drugs do not get them. Simultaneously, a high proportion of those who are given antimalarials do not in fact have malaria. Financial and other barriers mean that, in many settings, the majority of those with malaria, particularly the poorest, do not access formal healthcare, so the provision of free antimalarials via this route has only limited impact. The higher cost of ACT creates a market for fake drugs. Addressing these problems is now a priority. This review outlines current evidence, possible solutions and research priorities

Amplified melt and flow of the Greenland ice sheet driven by late-summer cyclonic rainfall

Intense rainfall events significantly affect Alpine and Alaskan glaciers through enhanced melting, ice-flow acceleration and subglacial sediment erosion, yet their impact on the Greenland ice sheet has not been assessed. Here we present measurements of ice velocity, subglacial water pressure and meteorological variables from the western margin of the Greenland ice sheet during a week of warm, wet cyclonic weather in late August and early September 2011. We find that extreme surface runoff from melt and rainfall led to a widespread acceleration in ice flow that extended 140 km into the ice-sheet interior. We suggest that the late-season timing was critical in promoting rapid runoff across an extensive bare ice surface that overwhelmed a subglacial hydrological system in transition to a less-efficient winter mode. Reanalysis data reveal that similar cyclonic weather conditions prevailed across southern and western Greenland during this time, and we observe a corresponding ice-flow response at all land- and marine-terminating glaciers in these regions for which data are available. Given that the advection of warm, moist air masses and rainfall over Greenland is expected to become more frequent in the coming decades, our findings portend a previously unforeseen vulnerability of the Greenland ice sheet to climate change

Determinants of the urinary and serum metabolome in children from six European populations

Background Environment and diet in early life can affect development and health throughout the life course. Metabolic phenotyping of urine and serum represents a complementary systems-wide approach to elucidate environment–health interactions. However, large-scale metabolome studies in children combining analyses of these biological fluids are lacking. Here, we sought to characterise the major determinants of the child metabolome and to define metabolite associations with age, sex, BMI and dietary habits in European children, by exploiting a unique biobank established as part of the Human Early-Life Exposome project (http://www.projecthelix.eu). Methods Metabolic phenotypes of matched urine and serum samples from 1192 children (aged 6–11) recruited from birth cohorts in six European countries were measured using high-throughput 1H nuclear magnetic resonance (NMR) spectroscopy and a targeted LC-MS/MS metabolomic assay (Biocrates AbsoluteIDQ p180 kit). Results We identified both urinary and serum creatinine to be positively associated with age. Metabolic associations to BMI z-score included a novel association with urinary 4-deoxyerythronic acid in addition to valine, serum carnitine, short-chain acylcarnitines (C3, C5), glutamate, BCAAs, lysophosphatidylcholines (lysoPC a C14:0, lysoPC a C16:1, lysoPC a C18:1, lysoPC a C18:2) and sphingolipids (SM C16:0, SM C16:1, SM C18:1). Dietary-metabolite associations included urinary creatine and serum phosphatidylcholines (4) with meat intake, serum phosphatidylcholines (12) with fish, urinary hippurate with vegetables, and urinary proline betaine and hippurate with fruit intake. Population-specific variance (age, sex, BMI, ethnicity, dietary and country of origin) was better captured in the serum than in the urine profile; these factors explained a median of 9.0% variance amongst serum metabolites versus a median of 5.1% amongst urinary metabolites. Metabolic pathway correlations were identified, and concentrations of corresponding metabolites were significantly correlated (r > 0.18) between urine and serum. Conclusions We have established a pan-European reference metabolome for urine and serum of healthy children and gathered critical resources not previously available for future investigations into the influence of the metabolome on child health. The six European cohort populations studied share common metabolic associations with age, sex, BMI z-score and main dietary habits. Furthermore, we have identified a novel metabolic association between threonine catabolism and BMI of children

Behavioural indicators of welfare in farmed fish

Behaviour represents a reaction to the environment as fish perceive it and is therefore a key element of fish welfare. This review summarises the main findings on how behavioural changes have been used to assess welfare in farmed fish, using both functional and feeling-based approaches. Changes in foraging behaviour, ventilatory activity, aggression, individual and group swimming behaviour, stereotypic and abnormal behaviour have been linked with acute and chronic stressors in aquaculture and can therefore be regarded as likely indicators of poor welfare. On the contrary, measurements of exploratory behaviour, feed anticipatory activity and reward-related operant behaviour are beginning to be considered as indicators of positive emotions and welfare in fish. Despite the lack of scientific agreement about the existence of sentience in fish, the possibility that they are capable of both positive and negative emotions may contribute to the development of new strategies (e. g. environmental enrichment) to promote good welfare. Numerous studies that use behavioural indicators of welfare show that behavioural changes can be interpreted as either good or poor welfare depending on the fish species. It is therefore essential to understand the species-specific biology before drawing any conclusions in relation to welfare. In addition, different individuals within the same species may exhibit divergent coping strategies towards stressors, and what is tolerated by some individuals may be detrimental to others. Therefore, the assessment of welfare in a few individuals may not represent the average welfare of a group and vice versa. This underlines the need to develop on-farm, operational behavioural welfare indicators that can be easily used to assess not only the individual welfare but also the welfare of the whole group (e. g. spatial distribution). With the ongoing development of video technology and image processing, the on-farm surveillance of behaviour may in the near future represent a low-cost, noninvasive tool to assess the welfare of farmed fish.Fundação para a Ciência e Tecnologia, Portugal [SFRH/BPD/42015/2007]info:eu-repo/semantics/publishedVersio