A Multi-Material Approach to Beam Hardening Correction and Calibration in X-Ray Microtomography

PhDX-ray microtomogaphy is a non-clinical, non-destructive, and quantitative technique for determining three-dimensional mineral concentration distributions in variably radiolucent samples with a spatial resolution on the micron scale. For reasons of practicality, particularly for longterm studies, it is often not possible or desirable to utilise a monochromatic X-ray source and so microtomography using a conventional impact-source X-ray generator to produce a polychromatic photon beam is carried out instead. The use of photons of multiple energies causes the production of projection artefacts arising from preferential absorption, which impair the greyscale accuracy of the resulting reconstruction and the material concentration measurements that are derived from the linear attenuation coefficients (LACs). The purpose of the project described in this thesis is to identify weaknesses in the current method of beam hardening correction and to develop and test a tomographic calibration and projection processing method which may demonstrably improve the quality of current beam hardening correction methods as used with the MuCAT microtomography equipment, which provides a worldclass impact-source microtomography research and production facility at Barts and The London School of Medicine and Dentistry. An overview of the physical basis of X-ray computed tomography and X-ray microtomography is given from first principles, and examples of quantitative applications of the techniques, which generally depend on accurate reconstruction of linear attenuation coefficient values, are discussed. The major sources of artefacts in X-ray microtomography are discussed, particularly those with a direct impact on reconstructed linear attenuation coefficient values. Beam hardening is identified as an error source of particular interest, with secondary research on the effects of any beam hardening correction method on the severity of Compton scatter artefacts, and a critical review is carried out of historical attempts to reduce or mitigate these artefacts, particularly the single-material parameter-optimisation approach in service at the beginning of the research project. A ‘carousel’ test piece comprising multiple attenuators of multiple materials along with attenuation optimisation software based on varying multiple system parameters in order to extend the functionality and usability of the existing correction model, and qualitative results have so far been gathered suggesting the use of this system over the pre-existing attenuation wedge and parameter-optimisation method. A study of the effects of tuning the photon energy to which calibrations are made is carried out, showing improved linear attenuation coefficient recovery at a higher energy than was previously believed to be optimal, and a significant effect arising from X-ray generator target evaporation leading to spatial changes and time-dependence of the target thickness parameter is measured, suggesting that automated calibration as a standard part of the measurement process is required. A stability experiment is carried out using this method in order to examine the possibility of inconsistency resulting from ageing of the filament cathode, which is found not to significantly impact the quality of results. An immersion tank is developed in order to ensure beam hardening correction validity in the case of dual-material specimens where a radiodensity-matching fluid can be provided and the sample is suitable for immersion. Experimental comparison using a commercial beam hardening calibration device as the specimen reveals significantly improved hydroxyapatite concentration measurement recovery. An in-scatter experiment was carried out on the immersion tank, and it was found that there was a significant scatter contribution when the tank was filled in the case where the sample thickness is much less than the tank thickness. Proposals are presented for further work to improve reconstruction quality through of scatter reduction techniques in impactsource microtomographic systems, and to utilise the immersion tank for in situ chemical erosion experiments. The effects of the improvements to the beam hardening process are demonstrated using a biological specimen to demonstrate qualitative changes in reconstruction, particularly in improved dark levels surrounding the specimen. A second experiment is carried out in order to test the reproducibility of results, which is found to be improved by approximately four times over the same dataset corrected using the pre-existingbeam-hardening calibration methodEngineering and Physical Sciences Research Council grant number EP/G007845/1

Immediate replacement of fishing with dairying by the earliest farmers of the NE Atlantic archipelagos

The appearance of farming, from its inception in the Near East around 12 000 years ago, finally reached the northwestern extremes of Europe by the fourth millennium BC or shortly thereafter. Various models have been invoked to explain the Neolithization of northern Europe; however, resolving these different scenarios has proved problematic due to poor faunal preservation and the lack of specificity achievable for commonly applied proxies. Here, we present new multi-proxy evidence, which qualitatively and quantitatively maps subsistence change in the northeast Atlantic archipelagos from the Late Mesolithic into the Neolithic and beyond. A model involving significant retention of hunter–gatherer–fisher influences was tested against one of the dominant adoptions of farming using a novel suite of lipid biomarkers, including dihydroxy fatty acids, ω-(o-alkylphenyl)alkanoic acids and stable carbon isotope signatures of individual fatty acids preserved in cooking vessels. These new findings, together with archaeozoological and human skeletal collagen bulk stable carbon isotope proxies, unequivocally confirm rejection of marine resources by early farmers coinciding with the adoption of intensive dairy farming. This pattern of Neolithization contrasts markedly to that occurring contemporaneously in the Baltic, suggesting that geographically distinct ecological and cultural influences dictated the evolution of subsistence practices at this critical phase of European prehistory

Gorilla in our midst: An online behavioral experiment builder

Behavioral researchers are increasingly conducting their studies online, to gain access to large and diverse samples that would be difficult to get in a laboratory environment. However, there are technical access barriers to building experiments online, and web browsers can present problems for consistent timing—an important issue with reaction-time-sensitive measures. For example, to ensure accuracy and test–retest reliability in presentation and response recording, experimenters need a working knowledge of programming languages such as JavaScript. We review some of the previous and current tools for online behavioral research, as well as how well they address the issues of usability and timing. We then present the Gorilla Experiment Builder (gorilla.sc), a fully tooled experiment authoring and deployment platform, designed to resolve many timing issues and make reliable online experimentation open and accessible to a wider range of technical abilities. To demonstrate the platform’s aptitude for accessible, reliable, and scalable research, we administered a task with a range of participant groups (primary school children and adults), settings (without supervision, at home, and under supervision, in both schools and public engagement events), equipment (participant’s own computer, computer supplied by the researcher), and connection types (personal internet connection, mobile phone 3G/4G). We used a simplified flanker task taken from the attentional network task (Rueda, Posner, & Rothbart, 2004). We replicated the Bconflict network^ effect in all these populations, demonstrating the platform’s capability to run reaction-time-sensitive experiments. Unresolved limitations of running experiments online are then discussed, along with potential solutions and some future features of the platform

Pots, plants and animals:broad-spectrum subsistence strategies in the Early Neolithic of the Moroccan Rif region

The transition from hunter-gathering to food-producing societies in the Mediterranean zone of north Africa was complex and variable, likely influenced by local ecological conditions as well as the socio-economic origins of the population. The adoption of domestic plants and animals was piecemeal, with hunting and gathering continuing as an important part of local subsistence strategies. Here, we investigate the timing and extent of the adoption of agricultural practices, namely herding and cultivation, in three diverse coastal and inland Early Neolithic sites in the Mediterranean Maghreb region, namely Ifri Oudadane, Ifri n’Etsedda and Hassi Ouenzga. Results from absorbed lipid residues extracted from 306 potsherds from these sites are correlated with information from faunal and archaeobotanical assemblages. Our findings suggest that agricultural practices, regarded as being of Neolithic origin, were never fully adopted in the Maghreb but rather that these farmer/foragers adopted a range of strategies including low-level food production (exploiting cereals and animal products, including meat and milk), gathering of wild plants and marine shellfish, and hunting both small and large sized game. These broad-spectrum farmer/foragers were clearly both flexible and resourceful and likely adapted their subsistence practices to maximise resource availability in an increasingly unpredictable environment

Holocene resource exploitation along the Nile:diet and subsistence strategies of Mesolithic and Neolithic societies at Khor Shambat 1, Sudan

The subsistence practices of Holocene communities living in the Nile Valley of Central Sudan are comparatively little known. Recent excavations at Khor Shambat, Sudan, have yielded well-defined Mesolithic and Neolithic stratigraphy. Here, for the first time, archaeozoological, palaeobotanical, phytolith and dental calculus studies are combined with lipid residue analysis of around 100 pottery fragments and comparative analysis of faunal remains and organic residues. This holistic approach provides valuable information on changes in adaptation strategies, from Mesolithic hunter-gatherers to Neolithic herders exploiting domesticates. A unique picture is revealed of the natural environment and human subsistence, demonstrating the potential wider value of combining multiple methods

Organic residues in archaeology - the highs and lows of recent research

YesThe analysis of organic residues from archaeological materials has become increasingly important to our understanding of ancient diet, trade and technology. Residues from diverse contexts have been retrieved and analysed from the remains of food, medicine and cosmetics to hafting material on stone arrowheads, pitch and tar from shipwrecks, and ancient manure from soils. Research has brought many advances in our understanding of archaeological, organic residues over the past two decades. Some have enabled very specific and detailed interpretations of materials preserved in the archaeological record. However there are still areas where we know very little, like the mechanisms at work during the formation and preservation of residues, and areas where each advance produces more questions rather than answers, as in the identification of degraded fats. This chapter will discuss some of the significant achievements in the field over the past decade and the ongoing challenges for research in this area.Full text was made available in the Repository on 15th Oct 2015, at the end of the publisher's embargo period

Latitudinal gradient in dairy production with the introduction of farming in Atlantic Europe

International audienceThe introduction of farming had far-reaching impacts on health, social structure and demography. Although the spread of domesticated plants and animals has been extensively tracked, it is unclear how these nascent economies developed within different environmental and cultural settings. Using molecular and isotopic analysis of lipids from pottery, here we investigate the foods prepared by the earliest farming communities of the European Atlantic seaboard. Surprisingly, we find an absence of aquatic foods, including in ceramics from coastal sites, except in the Western Baltic where this tradition continued from indigenous ceramic using hunter-gatherer-fishers. The frequency of dairy products in pottery increased as farming was progressively introduced along a northerly latitudinal gradient. This finding implies that early farming communities needed time to adapt their economic practices before expanding into more northerly areas. Latitudinal differences in the scale of dairy production might also have influenced the evolution of adult lactase persistence across Europe

Middle Neolithic pits and a burial at West Amesbury, Wiltshire

Excavations on the south-eastern slopes of King Barrow Ridge, 1.5 km east of Stonehenge, revealed five pits, a grave and other features of Middle Neolithic date. Analysis of the pit assemblages and the partial inhumation interred in the grave has provided insights into lifeways in this landscape in the late fourth millennium cal BC. Evidence suggests that the area was visited by a pastoralist, mobile community on a semi-regular basis for a significant period, in late autumn or winter. Selected remnants of craft-working and consumption were deposited in pits, before deliberate infilling. These depositions repeatedly memorialised activity on the hillside at a time of contemporary activity elsewhere on King Barrow Ridge and at the future site of Stonehenge. Middle Neolithic pits are present in significant numbers across King Barrow Ridge, and alongside pits in the Durrington area, form one of the densest concentrations of such activity in the region. Long distance mobility is suggested by the possible Irish origins of the inhumation, the first Middle Neolithic individual excavated in the environs of Stonehenge. Whilst of significance for understanding the Middle Neolithic in the WHS and the region, this research also hints at the roots of Late Neolithic monumentalisation of this landscape