ATD: a multiplatform for semiautomatic 3-D detection of kidneys and their pathology in real time

This research presents a novel multi-functional system for medical Imaging-enabled Assistive Diagnosis (IAD). Although the IAD demonstrator has focused on abdominal images and supports the clinical diagnosis of kidneys using CT/MRI imaging, it can be adapted to work on image delineation, annotation and 3D real-size volumetric modelling of other organ structures such as the brain, spine, etc. The IAD provides advanced real-time 3D visualisation and measurements with fully automated functionalities as developed in two stages. In the first stage, via the clinically driven user interface, specialist clinicians use CT/MRI imaging datasets to accurately delineate and annotate the kidneys and their possible abnormalities, thus creating “3D Golden Standard Models”. Based on these models, in the second stage, clinical support staff i.e. medical technicians interactively define model-based rules and parameters for the integrated “Automatic Recognition Framework” to achieve results which are closest to that of the clinicians. These specific rules and parameters are stored in “Templates” and can later be used by any clinician to automatically identify organ structures i.e. kidneys and their possible abnormalities. The system also supports the transmission of these “Templates” to another expert for a second opinion. A 3D model of the body, the organs and their possible pathology with real metrics is also integrated. The automatic functionality was tested on eleven MRI datasets (comprising of 286 images) and the 3D models were validated by comparing them with the metrics from the corresponding “3D Golden Standard Models”. The system provides metrics for the evaluation of the results, in terms of Accuracy, Precision, Sensitivity, Specificity and Dice Similarity Coefficient (DSC) so as to enable benchmarking of its performance. The first IAD prototype has produced promising results as its performance accuracy based on the most widely deployed evaluation metric, DSC, yields 97% for the recognition of kidneys and 96% for their abnormalities; whilst across all the above evaluation metrics its performance ranges between 96% and 100%. Further development of the IAD system is in progress to extend and evaluate its clinical diagnostic support capability through development and integration of additional algorithms to offer fully computer-aided identification of other organs and their abnormalities based on CT/MRI/Ultra-sound Imaging.

Some implications of a sample of practical Turing tests

A series of imitation games involving 3-participant (simultaneous comparison of two hidden entities) and 2-participant (direct interrogation of a hidden entity) were conducted at Bletchley Park on the 100th anniversary of Alan Turing’s birth: 23 June 2012. From the ongoing analysis of over 150 games involving (expert and non-expert, males and females, adults and child) judges, machines and hidden humans (foils for the machines), we present six particular conversations that took place between human judges and a hidden entity that produced unexpected results. From this sample we focus on features of Turing’s machine intelligence test that the mathematician/code breaker did not consider in his examination for machine thinking: the subjective nature of attributing intelligence to another mind.

Evidence of increased net ecosystem productivity associated with a longer vegetated season in a deciduous forest in south-central Indiana, USA

Observations of net ecosystem exchange (NEE) of carbon and its biophysical drivers have been collected at the AmeriFlux site in the Morgan-Monroe State Forest (MMSF) in Indiana, USA since 1998. Thus, this is one of the few deciduous forest sites in the world, where a decadal analysis on net ecosystem productivity (NEP) trends is possible. Despite the large interannual variability in NEP, the observations show a significant increase in forest productivity over the past 10 years (by an annual increment of about 10 g C m−2 yr−1). There is evidence that this trend can be explained by longer vegetative seasons, caused by extension of the vegetative activity in the fall. Both phenological and flux observations indicate that the vegetative season extended later in the fall with an increase in length of about 3 days yr−1 for the past 10 years. However, these changes are responsible for only 50% of the total annual gain in forest productivity in the past decade. A negative trend in air and soil temperature during the winter months may explain an equivalent increase in NEP through a decrease in ecosystem respiration.

Evolutionary and revolutionary effects of transcomputation

Mathematics in Defence 2011 Abstract. We review transreal arithmetic and present transcomplex arithmetic. These arithmetics have no exceptions. This leads to incremental improvements in computer hardware and software. For example, the range of real numbers, encoded by floating-point bits, is doubled when all of the Not-a-Number(NaN) states, in IEEE 754 arithmetic, are replaced with real numbers. The task of programming such systems is simplified and made safer by discarding the unordered relational operator,leaving only the operators less-than, equal-to, and greater than. The advantages of using a transarithmetic in a computation, or transcomputation as we prefer to call it, may be had by making small changes to compilers and processor designs. However, radical change is possible by exploiting the reliability of transcomputations to make pipelined dataflow machines with a large number of cores. Our initial designs are for a machine with order one million cores. Such a machine can complete the execution of multiple in-line programs each clock tick

Representing 3D shape and location

The 3D shape of an object and its 3D location have traditionally thought of as very separate entities, although both can be described within a single 3D coordinate frame. Here, 3D shape and location are considered as two aspects of a view-based approach to representing depth, avoiding the use of 3D coordinate frames.

Subdiffraction fluorescence imaging of biomolecular structure and distributions with quantum dots

We introduce semiconductor quantum dot-based fluorescence imaging with approximately 2-fold increased optical resolution in three dimensions as a method that allows both studying cellular structures and spatial organization of biomolecules in membranes and subcellular organelles. Target biomolecules are labelled with quantum dots via immunocytochemistry. The resolution enhancement is achieved by three-photon absorption of quantum dots and subsequent fluorescence emission from a higher-order excitonic state. Different from conventional multiphoton microscopy, this approach can be realized on any confocal microscope without the need for pulsed excitation light. We demonstrate quantum dot triexciton imaging (QDTI) of the microtubule network of U373 cells, 3D imaging of TNF receptor 2 on the plasma membrane of HeLa cells, and multicolor 3D imaging of mitochondrial cytochrome c oxidase and actin in COS-7 cells.

Intuitions in the Face of Diversity

In recent decades, intuitions' role in philosophy has been hotly debated. Many claim intuitions play an important role. Others, some armed with data, challenge the use of intuitions. This thesis reflects on this debate and advances the debate in two main ways. Having a clear understanding of the challenge which intuition-use in philosophy faces is important. Part I focuses on this. Chapters 1-2 introduce the topic of intuitions, motivate the methodological study of intuitions, and present the historical background to recent empirical challenges to intuition-use. Chapters 3-5 concern the contemporary challenge. I present the empirical evidence the challenge uses, present what I argue to be the strongest version of the challenge, and defend that challenge against some objections. How one characterises intuitions is incredibly important in philosophical methodology. If we are to properly evaluate philosophical methods vis-a-vis their use of something called intuitions { if we are to assess the empirical challenge { it is important to be clear exactly what we mean by `intuitions'. Part II focuses on this. Chapter 6 argues there is little consensus among philosophers as to what intuitions are and their role in philosophy. Chapter 7 questions whether philosophers have developed an idiolect in which `intuition' has distinctive meaning | as frequently supposed. Chapter 8 points out a common misunderstanding about intuitions in philosophy; using quantitative tools to challenge the idea that an increased use of `intuition' in philosophy is the result of an increased use of intuition. So, the developing picture is one of confusion, without a clear idea of what sense of `intuition' is important. Fortunately, Chapter 9 sets us back on the right track. It sets out a positive programme for evaluative methodology: methodologists should adopt a permissive conception of intuitions and make fine distinctions between different intuitions, so long as we can track those distinctions while philosophising.

Modularity and robustness of bone networks

Cortical bones, essential for mechanical support and structure in many animals, involve a large number of canals organized in intricate fashion. By using state-of-the art image analysis and computer graphics, the 3D reconstruction of a whole bone (phalange) of a young chicken was obtained and represented in terms of a complex network where each canal was associated to an edge and every confluence of three or more canals yielded a respective node. The representation of the bone canal structure as a complex network has allowed several methods to be applied in order to characterize and analyze the canal system organization and the robustness. First, the distribution of the node degrees (i.e. the number of canals connected to each node) confirmed previous indications that bone canal networks follow a power law, and therefore present some highly connected nodes (hubs). The bone network was also found to be partitioned into communities or modules, i.e. groups of nodes which are more intensely connected to one another than with the rest of the network. We verified that each community exhibited distinct topological properties that are possibly linked with their specific function. In order to better understand the organization of the bone network, its resilience to two types of failures (random attack and cascaded failures) was also quantified comparatively to randomized and regular counterparts. The results indicate that the modular structure improves the robustness of the bone network when compared to a regular network with the same average degree and number of nodes. The effects of disease processes (e. g., osteoporosis) and mutations in genes (e.g., BMP4) that occur at the molecular level can now be investigated at the mesoscopic level by using network based approaches.

Objective characterization of the course of the parasellar internal carotid artery using mathematical tools

Background Along the internal carotid artery (ICA), atherosclerotic plaques are often located in its cavernous sinus (parasellar) segments (pICA). Studies indicate that the incidence of pre-atherosclerotic lesions is linked with the complexity of the pICA; however, the pICA shape was never objectively characterized. Our study aims at providing objective mathematical characterizations of the pICA shape. Methods and results Three-dimensional (3D) computer models, reconstructed from contrast enhanced computed tomography (CT) data of 30 randomly selected patients (60 pICAs) were analyzed with modern visualization software and new mathematical algorithms. As objective measures for the pICA shape complexity, we provide calculations of curvature energy, torsion energy, and total complexity of 3D skeletons of the pICA lumen. We further measured the posterior knee of the so-called ""carotid siphon"" with a virtual goniometer and performed correlations between the objective mathematical calculations and the subjective angle measurements. Conclusions Firstly, our study provides mathematical characterizations of the pICA shape, which can serve as objective reference data for analyzing connections between pICA shape complexity and vascular diseases. Secondly, we provide an objective method for creating Such data. Thirdly, we evaluate the usefulness of subjective goniometric measurements of the angle of the posterior knee of the carotid siphon.

Three-dimensional description and mathematical characterization of the parasellar internal carotid artery in human infants

Inside the `cavernous sinus` or `parasellar region` the human internal carotid artery takes the shape of a siphon that is twisted and torqued in three dimensions and surrounded by a network of veins. The parasellar section of the internal carotid artery is of broad biological and medical interest, as its peculiar shape is associated with temperature regulation in the brain and correlated with the occurrence of vascular pathologies. The present study aims to provide anatomical descriptions and objective mathematical characterizations of the shape of the parasellar section of the internal carotid artery in human infants and its modifications during ontogeny. Three-dimensional (3D) computer models of the parasellar section of the internal carotid artery of infants were generated with a state-of-the-art 3D reconstruction method and analysed using both traditional morphometric methods and novel mathematical algorithms. We show that four constant, demarcated bends can be described along the infant parasellar section of the internal carotid artery, and we provide measurements of their angles. We further provide calculations of the curvature and torsion energy, and the total complexity of the 3D skeleton of the parasellar section of the internal carotid artery, and compare the complexity of this in infants and adults. Finally, we examine the relationship between shape parameters of the parasellar section of the internal carotid artery in infants, and the occurrence of intima cushions, and evaluate the reliability of subjective angle measurements for characterizing the complexity of the parasellar section of the internal carotid artery in infants. The results can serve as objective reference data for comparative studies and for medical imaging diagnostics. They also form the basis for a new hypothesis that explains the mechanisms responsible for the ontogenetic transformation in the shape of the parasellar section of the internal carotid artery.

3D face computational photography using PCA spaces

In this paper, we present a 3D face photography system based on a facial expression training dataset, composed of both facial range images (3D geometry) and facial texture (2D photography). The proposed system allows one to obtain a 3D geometry representation of a given face provided as a 2D photography, which undergoes a series of transformations through the texture and geometry spaces estimated. In the training phase of the system, the facial landmarks are obtained by an active shape model (ASM) extracted from the 2D gray-level photography. Principal components analysis (PCA) is then used to represent the face dataset, thus defining an orthonormal basis of texture and another of geometry. In the reconstruction phase, an input is given by a face image to which the ASM is matched. The extracted facial landmarks and the face image are fed to the PCA basis transform, and a 3D version of the 2D input image is built. Experimental tests using a new dataset of 70 facial expressions belonging to ten subjects as training set show rapid reconstructed 3D faces which maintain spatial coherence similar to the human perception, thus corroborating the efficiency and the applicability of the proposed system.

Computer-aided design decision support: interfacing knowledge and information

Computer-aided design decision support has proved to be an elusive and intangible project for many researchers as they seek to encapsulate information and knowledge-based systems as useful multifunctional data structures. Definitions of ‘knowledge', ‘information', ‘facts', and ‘data' become semantic footballs in the struggle to identify what designers actually do, and what level of support would suit them best, and how that support might be offered. The Construction Primer is a database-drivable interactive multimedia environment that provides readily updated access to many levels of information aimed to suit students and practitioners alike. This is hardly a novelty in itself. The innovative interface and metadata structures, however, combine with the willingness of national building control legislators, standards authorities, materials producers, building research organisations, and specification services to make the Construction Primer a versatile design decision support vehicle. It is both compatible with most working methodologies while remaining reasonably future-proof. This paper describes the structure of the project and highlights the importance of sound planning and strict adhesion to library-standard metadata protocols as a means to avoid the support becoming too specific or too paradigmatic.

Observations of ground-foraging by Rufous-Banded Honeyeaters Conopophila albogularis

Observations of Rufous-banded Honeyeaters Conopophila albogularis ground-foraging amongst tall grass near Darwin are described. Previous published studies indicate that ground-foraging is rare for this species. These observations suggest that ground-foraging may constitute an established foraging behaviour at certain times.

Soft tissue modelling for haptic rendering in virtual environments

This paper focuses on the development of a haptic recording and modelling system. Currently being evaluated for multiple uses in surgery and manufacturing, this recording system evaluates haptic data captured via a robotic ann coupled with real time high-resolution load cell. This data is then analysed and validated against previous samples and a generated model before being logged for playback during simulation and training of a human operator. 3D models of point force interactions are created allowing unique visuals to be presented to a user. Primarily designed for the medical field, recorded results of soft tissue cutting have been presented.

Diameter variations of irregular fibers under different tensions

The cross-section area of animal fibers varies along the fiber length, and this geometrical irregularity has a major impact on the mechanical properties of those fibers. In practice fibers are often subjected to tensile stresses during processing and application, which may change fiber cross-section area. It is thus necessary to examine geometrical irregularity of fibers under tension. In this study, scoured animal fibers were subjected to different tensile loading using a Single Fiber Analyzer (SIFAN) instrument. The 3D images of the fiber specimens were first constructed, and then along-fiber diameter irregularities of the specimens were analyzed for different levels of tensile loading. The changes in effective fineness of the fiber specimens were also discussed. The results indicate that for the wool fibers examined, there is considerable discrepancy in the fiber diameter results obtained from the commonly used single scan along fiber length and that from multiple scans at different rotational angles, and that the diameter variation along fiber length increases as fiber tension increases. The results also show that when diameter reduction treatments are applied to wool by stretching, the reduced average fiber diameter is associated with an increase in both within-fiber and between-fiber diameter variations. So in terms of effective fineness, the change is much smaller than the difference between the average diameters of the parent and treated wool. These results have significant implications for improving the accuracy of fiber diameter measurement and evaluation.