Distinguishing between mean-field, moment dynamics and stochastic descriptions of birth-death-movement processes

Mathematical descriptions of birth–death–movement processes are often calibrated to measurements from cell biology experiments to quantify tissue growth rates. Here we describe and analyze a discrete model of a birth–death-movement process applied to a typical two–dimensional cell biology experiment. We present three different descriptions of the system: (i) a standard mean–field description which neglects correlation effects and clustering; (ii) a moment dynamics description which approximately incorporates correlation and clustering effects, and; (iii) averaged data from repeated discrete simulations which directly incorporates correlation and clustering effects. Comparing these three descriptions indicates that the mean–field and moment dynamics approaches are valid only for certain parameter regimes, and that both these descriptions fail to make accurate predictions of the system for sufficiently fast birth and death rates where the effects of spatial correlations and clustering are sufficiently strong. Without any method to distinguish between the parameter regimes where these three descriptions are valid, it is possible that either the mean–field or moment dynamics model could be calibrated to experimental data under inappropriate conditions, leading to errors in parameter estimation. In this work we demonstrate that a simple measurement of agent clustering and correlation, based on coordination number data, provides an indirect measure of agent correlation and clustering effects, and can therefore be used to make a distinction between the validity of the different descriptions of the birth–death–movement process.

Segmentation of cone-beam CT using a hidden Markov random field with informative priors

Cone-beam computed tomography (CBCT) has enormous potential to improve the accuracy of treatment delivery in image-guided radiotherapy (IGRT). To assist radiotherapists in interpreting these images, we use a Bayesian statistical model to label each voxel according to its tissue type. The rich sources of prior information in IGRT are incorporated into a hidden Markov random field model of the 3D image lattice. Tissue densities in the reference CT scan are estimated using inverse regression and then rescaled to approximate the corresponding CBCT intensity values. The treatment planning contours are combined with published studies of physiological variability to produce a spatial prior distribution for changes in the size, shape and position of the tumour volume and organs at risk. The voxel labels are estimated using iterated conditional modes. The accuracy of the method has been evaluated using 27 CBCT scans of an electron density phantom. The mean voxel-wise misclassification rate was 6.2\%, with Dice similarity coefficient of 0.73 for liver, muscle, breast and adipose tissue. By incorporating prior information, we are able to successfully segment CBCT images. This could be a viable approach for automated, online image analysis in radiotherapy.

A novel representation of bioacoustic events for content-based search in field audio data

Bioacoustic data can provide an important base for environmental monitoring. To explore a large amount of field recordings collected, an automated similarity search algorithm is presented in this paper. A region of an audio defined by frequency and time bounds is provided by a user; the content of the region is used to construct a query. In the retrieving process, our algorithm will automatically scan through recordings to search for similar regions. In detail, we present a feature extraction approach based on the visual content of vocalisations – in this case ridges, and develop a generic regional representation of vocalisations for indexing. Our feature extraction method works best for bird vocalisations showing ridge characteristics. The regional representation method allows the content of an arbitrary region of a continuous recording to be described in a compressed format.

Dependence of residual amplitude noise in electro-optic phase modulators on the intensity distribution of the incident field

Our results demonstrate that photorefractive residual amplitude modulation (RAM) noise in electro-optic modulators (EOMs) can be reduced by modifying the incident beam intensity distribution. Here we report an order of magnitude reduction in RAM when beams with uniform intensity (flat-top) profiles, generated with an LCOS-SLM, are used instead of the usual fundamental Gaussian mode (TEM00). RAM arises from the photorefractive amplified scatter noise off the defects and impurities within the crystal. A reduction in RAM is observed with increasing intensity uniformity (flatness), which is attributed to a reduction in space charge field on the beam axis. The level of RAM reduction that can be achieved is physically limited by clipping at EOM apertures, with the observed results agreeing well with a simple model. These results are particularly important in applications where the reduction of residual amplitude modulation to 10^-6 is essential.

Incorporating spatial correlations into multispecies mean-field models

In biology, we frequently observe different species existing within the same environment. For example, there are many cell types in a tumour, or different animal species may occupy a given habitat. In modelling interactions between such species, we often make use of the mean field approximation, whereby spatial correlations between the locations of individuals are neglected. Whilst this approximation holds in certain situations, this is not always the case, and care must be taken to ensure the mean field approximation is only used in appropriate settings. In circumstances where the mean field approximation is unsuitable we need to include information on the spatial distributions of individuals, which is not a simple task. In this paper we provide a method that overcomes many of the failures of the mean field approximation for an on-lattice volume-excluding birth-death-movement process with multiple species. We explicitly take into account spatial information on the distribution of individuals by including partial differential equation descriptions of lattice site occupancy correlations. We demonstrate how to derive these equations for the multi-species case, and show results specific to a two-species problem. We compare averaged discrete results to both the mean field approximation and our improved method which incorporates spatial correlations. We note that the mean field approximation fails dramatically in some cases, predicting very different behaviour from that seen upon averaging multiple realisations of the discrete system. In contrast, our improved method provides excellent agreement with the averaged discrete behaviour in all cases, thus providing a more reliable modelling framework. Furthermore, our method is tractable as the resulting partial differential equations can be solved efficiently using standard numerical techniques.

Acute hamstring strain injury in track and field athletes : a 3-year observational study at the Penn Relay Carnival

Purpose To observe the incidence rates of hamstring strain injuries (HSIs) across different competition levels and ages during the Penn Relays Carnival. Methods Over a 3-year period all injuries treated by the medical staff were recorded. The type of injury, anatomic location, event in which the injury occurred, competition level and demographic data were documented. Absolute and relative HSI (per 1000 participants) were determined and odds ratios (OR) were calculated between genders, competition levels and events. Results Throughout the study period 48,473 athletes registered to participate in the Penn Relays Carnival, with 118 HSIs treated by the medical team. High school females displayed lesser risk of HSI than high school males (OR = 0.55, p = 0.021), and masters athletes were more likely than high school (OR = 4.26, p < 0.001) and college (OR = 3.55, p = 0.001) level athletes to suffer a HSI. The 4x400m relay displayed a greater likelihood of HSI compared to the 4x100m relay (OR = 1.77, p = 0.008). Conclusions High school males and masters levels athletes are most likely to suffer HSI, and there is higher risk in 400m events compared to 100m events.

Peripheral refraction patterns out to large field angles

Purpose To investigate hyperopic shifts and the oblique (or 45-degree/135-degree) component of astigmatism at large angles in the horizontal visual field using the Hartmann-Shack technique. Methods The adult participants consisted of 6 hypermetropes, 13 emmetropes and 11 myopes. Measurements were made with a modified COAS-HD Hartmann-Shack aberrometer across T60 degrees along the horizontal visual field in 5-degree steps. Eyes were dilated with 1% cyclopentolate. Peripheral refraction was estimated as mean spherical (or spherical equivalent) refraction, with/against the rule of astigmatism and oblique astigmatism components, and as horizontal and vertical refraction components based on 3-mm major diameter elliptical pupils. Results Thirty percent of eyes showed a pattern that was a combination of type IV and type I patterns of Rempt et al. (Rempt F, Hoogerheide J, Hoogenboom WP. Peripheral retinoscopy and the skiagram. Ophthalmologica 1971;162:1Y10), which shows the characteristics of type IV (relative hypermetropia along the vertical meridian and relative myopia along the horizontal meridian) out to an angle of between 40 and 50 degrees before behaving like type I (both meridians show relative hypermetropia). We classified this pattern as type IV/I. Seven of 13 emmetropes had this pattern. As a group, there was no significant variation of the oblique component of astigmatism with angle, but about one-half of the eyes showed significant positive slopes (more positive or less negative values in the nasal field than in the temporal field) and one-fourth showed significant negative slopes. Conclusions It is often considered that a pattern of relative peripheral hypermetropia predisposes to the development of myopia. In this context, the finding of a considerable portion of emmetropes with the IV/I pattern suggests that it is unlikely that refraction at visual field angles beyond 40 degrees from fixation contributes to myopia development.

Students' cultural capital : a study of assessment for learning as a field of exchange

This study was conducted within the context of a flexible education institution where conventional educational assessment practices and tests fail to recognise and assess the creativity and cultural capital of a cohort of marginalised young people. A new assessment model which included an electronic-portfolio-social-networking system (EPS) was developed and trialled to identify and exhibit evidence of students' learning. The study aimed to discern unique forms of cultural capital (Bourdieu, 1986) possessed by students who attend the Edmund Rice Education Australia Flexible Learning Centre Network (EREAFLCN). The EPS was trialled at the case study schools in an intervention and developed a space where students could make evident culturally specific forms of capital and funds of knowledge (Gonzalez, Moll, & Amanti, 2005). These resources were evaluated, modified and developed through dialogic processes utilising assessment for learning approaches (Qualifications and Curriculum Development Agency, 2009) in online and classroom settings. Students, peers and staff engaged in the recognition, judgement, revision and evaluation of students' cultural capital in a subfield of exchange (Bourdieu, 1990). The study developed the theory of assessment for learning as a field of exchange incorporating an online system as a teaching and assessment model. The term efield has been coined to describe this particular capital exchange model. A quasi-ethnographic approach was used to develop a collective case study (Stake, 1995). This case study involved an in-depth exploration of five students' forms of cultural capital and the ways in which this capital could be assessed and exchanged using the efield model. A comparative analysis of the five cases was conducted to identify the emergent issues of students' recognisable cultural capital resources and the processes of exchange that can be facilitated to acquire legitimate credentials for these students in the Australian field of education. The participants in the study were young people at two EREAFLC schools aged between 12 and 18 years. Data was collected through interviews, observations and examination of documents made available by the EREAFLCN. The data was coded and analysed using a theoretical framework based on Bourdieu's analytical tools and a sociocultural psychology theoretical perspective. Findings suggest that processes based on dialogic relationships can identify and recognise students' forms of cultural capital that are frequently misrecognised in mainstream school environments. The theory of assessment for learning as a field of exchange was developed into praxis and integrated in an intervention. The efield model was found to be an effective sociocultural tool in converting and exchanging students' capital resources for legitimated cultural and symbolic capital in the field of education.

Hemi-field and full-field form-deprivation induce timing changes in multifocal ERG responses in chick

Purpose: In animal models hemi-field deprivation results in localised, graded vitreous chamber elongation and presumably deprivation induced localised changes in retinal processing. The aim of this research was to determine if there are variations in ERG responses across the retina in normal chick eyes and to examine the effect of hemi-field and full-field deprivation on ERG responses across the retina and at earlier times than have previously been examined electrophysiologically. Methods: Chicks were either untreated, wore monocular full-diffusers or half-diffusers (depriving nasal retina) (n = 6-8 each group) from day 8. mfERG responses were measured using the VERIS mfERG system across the central 18.2º× 16.7º (H × V) field. The stimulus consisted of 61 unscaled hexagons with each hexagon modulated between black and white according to a pseudorandom binary m-sequence. The mfERG was measured on day 12 in untreated chicks, following 4 days of hemi-field diffuser wear, and 2, 48 and 96 h after application of full-field diffusers. Results: The ERG response of untreated chick eyes did not vary across the measured field; there was no effect of retinal location on the N1-P1 amplitude (p = 0.108) or on P1 implicit time (p > 0.05). This finding is consistent with retinal ganglion cell density of the chick varying by only a factor of two across the entire retina. Half-diffusers produced a ramped retina and a graded effect of negative lens correction (p < 0.0001); changes in retinal processing were localized. The untreated retina showed increasing complexity of the ERG waveform with development; form-deprivation prevented the increasing complexity of the response at the 2, 48 and 96 h measurement times and produced alterations in response timing. Conclusions: Form-deprivation and its concomitant loss of image contrast and high spatial frequency images prevented development of the ERG responses, consistent with a disruption of development of retinal feedback systems. The characterisation of ERG responses in normal and deprived chick eyes across the retina allows the assessment of concurrent visual and retinal manipulations in this model. (Ophthalmic & Physiological Optics © 2013 The College of Optometrists.)

Perdido : the first Smart Field in the western hemisphere

Located in the Gulf of Mexico in nearly 8,000 feet of water, the Perdido development is the world’s deepest spar and Shell’s first Smart Field in the Western hemisphere. Jointly developed by Shell, BP, and Chevron, the spar and the subsea equipment connected to it will eventually capture approximately an order of magnitude more data than is collected from any other Shell-designed and managed development currently operating in the Gulf of Mexico. This paper will describe Shell’s Smart Fields design philosophy, briefly explain the five design elements that underpin “smartness” in Shell’s North and South American operations—specifically, remote assisted operations, exception-based surveillance, collaborative work environments, hydrocarbon development tools and workflows, and Smart Fields Foundation IT infrastructure—and shed light on the process by which a highly customized Smart Fields development and management plan was put together for Perdido.

A field experiment in moral suasion and tax compliance focusing on underdeclaration and overdeduction

One of very few field experiments in tax compliance, this study generates a unique data set on Swiss taxpayers’ underdeclaration of income and wealth and overdeduction of tax credits by obtaining exclusive access to tax-return corrections made by the tax administration. Using this commune-level data from Switzerland, it explores the influence on tax compliance of moral suasion, introduced through a treatment in which taxpayers receive a letter containing normative appeals signed by the commune’s fiscal commissioner. This letter also serves to operationalize elements of social identity and (mutual) trust. Interestingly, the results not only echo the earlier finding that moral suasion has barely any effect on taxpayer compliance, but show clear differences between underdeclaration and overdeduction.

Sexualities and sensitivities: Queer(y)ing the ethics of youth research in the field

In contemporary Western societies, the years between childhood and young adulthood are commonly understood to be (trans)formative in the reflexive project of sexual self-making (Russell et al. 2012). As sexual subjects in the making, youthful bodies, desires and sexual activities are often perceived as both volatile and vulnerable, thus subjected to instruction and discipline, protection and surveillance. Accordingly, young people’s sexual proximities are closely monitored by social institutions and ‘(hetero)normalising regimes’ (Warner 1999) for any signs that may compromise the end goal of development—a ‘normal’ reproductive heterosexual monogamous adult...

12 principles for the effective supervision of creative practice higher research degrees, dispatches from the field

In late 2012 and early 2013 we interviewed 25 experienced and early career supervisors of creative practice higher research degrees. This journey spanned five universities and a broad range of disciplines including visual art, music, performing art, new media, creative writing, fashion, graphic design, interaction design and interior design. Some of the supervisors we interviewed were amongst the first to complete and supervise practice-led and practice-based PhDs; some have advocated for and defined this emergent field; and some belong to the next generation of supervisors who have confidently embarked on this exciting and challenging path. Their reflections have brought to light many insights gained over the past decade. Here we have drawn together common themes into a collection of principles and best practice examples. We present them as advice rather than rules, as one thing that the supervisors were unanimous about is the need to avoid proscriptive models and frameworks, and to foster creativity and innovation in what is still an emergent field of postgraduate supervision. It is with thanks to all of the supervisors who contributed to these conversations, and their generosity in sharing their practices, that we present their advice, exemplars and case studies.

Pupil shape as viewed along the horizontal visual field

Purpose: Changes in pupil size and shape are relevant for peripheral imagery by affecting aberrations and how much light enters and/or exits the eye. The purpose of this study is to model the pattern of pupil shape across the complete horizontal visual field and to show how the pattern is influenced by refractive error. Methods: Right eyes of thirty participants were dilated with 1% cyclopentolate and images were captured using a modified COAS-HD aberrometer alignment camera along the horizontal visual field to ±90°. A two lens relay system enabled fixation at targets mounted on the wall 3m from the eye. Participants placed their heads on a rotatable chin rest and eye rotations were kept to less than 30°. Best-fit elliptical dimensions of pupils were determined. Ratios of minimum to maximum axis diameters were plotted against visual field angle. Results: Participants’ data were well fitted by cosine functions, with maxima at (–)1° to (–)9° in the temporal visual field and widths 9% to 15% greater than predicted by the cosine of the field angle . Mean functions were 0.99cos[( + 5.3)/1.121], R2 0.99 for the whole group and 0.99cos[( + 6.2)/1.126], R2 0.99 for the 13 emmetropes. The function peak became less temporal, and the width became smaller, with increase in myopia. Conclusion: Off-axis pupil shape changes are well described by a cosine function which is both decentered by a few degrees and flatter by about 12% than the cosine of the viewing angle, with minor influences of refraction.

The velocity synchronous discrete Fourier transform for order tracking in the field of rotating machinery

Diagnostics of rotating machinery has developed significantly in the last decades, and industrial applications are spreading in different sectors. Most applications are characterized by varying velocities of the shaft and in many cases transients are the most critical to monitor. In these variable speed conditions, fault symptoms are clearer in the angular/order domains than in the common time/frequency ones. In the past, this issue was often solved by synchronously sampling data by means of phase locked circuits governing the acquisition; however, thanks to the spread of cheap and powerful microprocessors, this procedure is nowadays rarer; sampling is usually performed at constant time intervals, and the conversion to the order domain is made by means of digital signal processing techniques. In the last decades different algorithms have been proposed for the extraction of an order spectrum from a signal sampled asynchronously with respect to the shaft rotational velocity; many of them (the so called computed order tracking family) use interpolation techniques to resample the signal at constant angular increments, followed by a common discrete Fourier transform to shift from the angular domain to the order domain. A less exploited family of techniques shifts directly from the time domain to the order spectrum, by means of modified Fourier transforms. This paper proposes a new transform, named velocity synchronous discrete Fourier transform, which takes advantage of the instantaneous velocity to improve the quality of its result, reaching performances that can challenge the computed order tracking.