'Introducing Dendritic Cells as a Novel Immune-Inspired Algorithm for Anomaly Detection'

Abstract. Dendritic cells are antigen presenting cells that provide a vital link between the innate and adaptive immune system. Research into this family of cells has revealed that they perform the role of coordinating T-cell based immune responses, both reactive and for generating tolerance. We have derived an algorithm based on the functionality of these cells, and have used the signals and differentiation pathways to build a control mechanism for an artificial immune system. We present our algorithmic details in addition to some preliminary results, where the algorithm was applied for the purpose of anomaly detection. We hope that this algorithm will eventually become the key component within a large, distributed immune system, based on sound immunological concepts.

Reactive Attachment Disorder in infants in foster care and associated mental health and cognitive functioning

Background: Reactive attachment disorder (RAD) has been described as one of the least researched and most poorly understood psychiatric disorders (Chaffin et al., 2006). Despite this, given what is known about maltreatment and attachment, it is likely that RAD has profound consequences for child development. Very little is known about the prevalence and stability of RAD symptoms over time. Until recently it has been difficult to investigate the presence of RAD due to limited measures for informing a diagnosis. However this study utilised a new observational tool Method: A cross sectional study design with a one-year follow-up explored RAD symptoms in maltreated infants in Scotland (n=55, age range= 16-62 months) and associated mental health and cognitive functioning. The study utilised the Rating of Inhibited Attachment Behavior Scale (Corval, et al., unpublished 2014) that has recently been developed by experts in the field along side The Disturbances of Attachment Interview (Smyke & Zeanah, 1999). Children were recruited as part of the BeST trial, whereby all infants who came in to the care of the local authority in Glasgow due to child protection concerns were invited to participate. The study sample was representative of the larger pool of data in terms of age, gender, mental health and cognitive functioning. Results: The sample was found to be representative of the population of maltreated children from which it was derived. Prevalence of RAD was found to be 7.3% (n=3, 95% CI [0.43 – 14.17]) at T1, when children are first placed in to foster care. At T2, following one year in improved care conditions, 4.3% (n=2, 95% CI [below 0 – 10.16]) met a borderline RAD diagnosis. Levels of observed RAD symptoms decreased significantly at T2 in comparison to T1 but carer reported symptoms of RAD did not. Children whose RAD symptoms did not improve were found to be significantly older and showed less prosocial behaviour. RAD was associated with some mental health and cognitive difficulties. Lower Verbal IQ and unexpectedly, prosocial behaviour were found to predict RAD symptoms. Conclusions: The preliminary findings have added to the developing understanding of RAD symptoms and associated difficulties however further exploration of RAD in larger samples would be invaluable.

Oxidative stress and its haemodynamic consequences in chronic kidney disease

Chronic kidney disease (CKD) is associated with increased cardiovascular risk in comparison with the general population. This can be observed even in the early stages of CKD, and rises in proportion to the degree of renal impairment. Not only is cardiovascular disease (CVD) more prevalent in CKD, but its nature differs too, with an excess of morbidity and mortality associated with congestive cardiac failure, arrhythmia and sudden death, as well as the accelerated atherosclerosis which is also observed. Conventional cardiovascular risk factors such as hypertension, dyslipidaemia, obesity, glycaemia and smoking, are highly prevalent amongst patients with CKD, although in many of these examples the interaction between risk factor and disease differs from that which exists in normal renal function. Nevertheless, the extent of CVD cannot be fully explained by these conventional risk factors, and non-conventional factors specific to CKD are now recognised to contribute to the burden of CVD. Oxidative stress is a state characterised by excessive production of reactive oxygen species (ROS) and other radical species, a reduction in the capacity of antioxidant systems, and disturbance in normal redox homeostasis with depletion of protective vascular signalling molecules such as nitric oxide (NO). This results in oxidative damage to macromolecules such as lipids, proteins and DNA which can alter their functionality. Moreover, many enzymes are sensitive to redox regulation such that oxidative modification to cysteine thiol groups results in activation of signalling cascades which result in adverse cardiovascular effects such as vascular and endothelial dysfunction. Endothelial dysfunction and oxidative stress are present in association with many conventional cardiovascular risk factors, and can be observed even prior to the development of overt, clinical, vascular pathology, suggesting that these phenomena represent the earliest stages of CVD. In the presence of CKD, there is increased ROS production due to upregulated NADPH oxidase (NOX), increase in a circulating asymmetric dimethylarginine (ADMA), uncoupling of endothelial nitric oxide synthase (eNOS) as well as other mechanisms. There is also depletion in exogenous antioxidants such as ascorbic acid and tocopherol, and a reduction in activity of endogenous antioxidant systems regulated by the master gene regulator Nrf-2. In previous studies, circulating markers of oxidative stress have been shown to be increased in CKD, together with a reduction in endothelial function in a stepwise fashion relating to the severity of renal impairment. Not only is CVD linked to oxidative stress, but the progression of CKD itself is also in part dependent on redox sensitive mechanisms. For example, administration of the ROS scavenger tempol attenuates renal injury and reduces renal fibrosis seen on biopsy in a mouse model of CKD, whilst conversely, supplementation with the NOS inhibitor L-NAME causes proteinuria and renal impairment. Previous human studies examining the effect of antioxidant administration on vascular and renal function have been conflicting however. The work contained in this thesis therefore examines the effect of antioxidant administration on vascular and endothelial function in CKD. Firstly, 30 patients with CKD stages 3 – 5, and 20 matched hypertensive controls were recruited. Participants with CKD had lower ascorbic acid, higher TAP and ADMA, together with higher augmentation index and pulse wave velocity. There was no difference in baseline flow mediated dilatation (FMD) between groups. Intravenous ascorbic acid increased TAP and O2-, and reduced central BP and augmentation index in both groups, and lowered ADMA in the CKD group only. No effect on FMD was observed. The effects of ascorbic acid on kidney function was then investigated, however this was hindered by the inherent drawbacks of existing methods of non-invasively measuring kidney function. Arterial spin labelling MRI is an emerging imaging technique which allows measurement of renal perfusion without administration of an exogenous contrast agent. The technique relies upon application of an inversion pulse to blood within the vasculature proximal to the kidneys, which magnetically labels protons allowing measurement upon transit to the kidney. At the outset of this project local experience using ASL MRI was limited and there ensued a prolonged pre-clinical phase of testing with the aim of optimising imaging strategy. A study was then designed to investigate the repeatability of ASL MRI in a group of 12 healthy volunteers with normal renal function. The measured T1 longitudinal relaxation times and ASL MRI perfusion values were in keeping with those found in the literature; T1 time was 1376 ms in the cortex and 1491 ms in the whole kidney ROI, whilst perfusion was 321 mL/min/100g in the cortex, and 228 mL/min/100g in the whole kidney ROI. There was good reproducibility demonstrated on Bland Altman analysis, with a CVws was 9.2% for cortical perfusion and 7.1% for whole kidney perfusion. Subsequently, in a study of 17 patients with CKD and 24 healthy volunteers, the effects of ascorbic acid on renal perfusion was investigated. Although no change in renal perfusion was found following ascorbic acid, it was found that ASL MRI demonstrated significant differences between those with normal renal function and participants with CKD stages 3 – 5, with increased cortical and whole kidney T1, and reduced cortical and whole kidney perfusion. Interestingly, absolute perfusion showed a weak but significant correlation with progression of kidney disease over the preceding year. Ascorbic acid was therefore shown to have a significant effect on vascular biology both in CKD and in those with normal renal function, and to reduce ADMA only in patients with CKD. ASL MRI has shown promise as a non-invasive investigation of renal function and as a biomarker to identify individuals at high risk of progressive renal impairment.

Long-Term In Situ Survey of Reactive Iron Concentrations at the EMSO-Azores Observatory

A study of the temporal dynamics of iron concentrations and temperature on a faunal assemblage at the Lucky Strike vent was performed using the Tempo ecological module at the EMSO-Azores deep-sea observatory. The CHEMINI in situ analyzer was implemented on this structure to determine reactive iron concentrations in unfiltered seawater samples along with a temperature probe. Stability tests were performed on the CHEMINI analyzer before deployment (optical module, hyperbaric tests, and deep-sea calibration) for long-term in situ analysis of reactive iron (six months, 2013–2014) at the Tour Eiffel active edifice. Recorded daily, the in situ standard (25 \mu mol.L {}^{-1} ) showed excellent reproducibility (1.07%, n=522 ), confirming satisfactory analytical performance of the CHEMINI analyzer and thus validating the iron concentrations measured by the instrument. Furthermore, the analyzer proved to be reliable and robust over time. The averaged reactive iron concentration for the six-month period remained low ([Fe] =text{7.12}\pm text{2.11} \mu mol.L {}^{-1} , n=519 ), but showed some noticeable variations with temperature. Reactive iron concentrations and temperature were significantly correlated emphasizing reactive iron stabilization over the time of deployment. Period spectra indicated strong tidal influence and relevant frequencies of four to five days for both variables.

Reactive clusters on a membrane

We investigate the reaction dynamics of diffusive molecules with immobile binding partners. The fixed reactants build clusters that comprise just a few tens of molecules, which leads to small cluster sizes. These molecules participate in the reaction only if they are activated. The dynamics of activation is mapped to a time-dependent size of an active region within the cluster. We focus on the deterministic description of the dynamics of a single cluster. The spatial setup accounts for one of the most important determinants of the dynamics of a cluster, i.e. diffusional transport of reaction partners toward or away from the active region of the cluster. We provide numerical and analytical evidence that diffusion influences decisively the dynamic regimes of the reactions. The application of our methods to intracellular Ca²⁺ dynamics shows that large local concentrations saturate the Ca²⁺ feedback to the channel state control. That eliminates oscillations depending on this feedback.

A Staggered Decameric Assembly of Human C-Reactive Protein Stabilized by Zinc Ions Revealed by X-ray Crystallography

International audience

Association between ferritin, high sensitivity c-reactive protein (hsCRP) and relative abundance of Hepcidin mRNA with the risk of type 2 diabetes in obese subjects

Obesity and Type 2 diabetes mellitus share a strong pro-inflammatory profile. It has been observed that iron is a risk factor in the development of type 2 diabetes. The aim of this study was to evaluate the relationship between iron nutritional status and inflammation with the risk of type 2 diabetes development in obese subjects. We studied 30 obese men with type 2 diabetes (OBDM); 30 obese subjects without diabetes (OB) and 30 healthy subjects (Cn). We isolated peripheral mononuclear cells (PMCs) and challenged them with high Fe concentrations. Total mRNA was isolated and relative abundance of TNF-αIL-6 and hepcidin were determined by qPCR. Iron status, biochemical, inflammatory and oxidative stress parameters were also characterized. OBDM and OB patients showed increased hsCRP levels compared to the Cn group. OBDM subjects showed higher levels of ferritin than the Cn group. TNF-α and IL-6 mRNA relative abundances were increased in OBDM PMCs treated with high/Fe. Hepcidin mRNA was increased with basal and high iron concentration. We found that the highest quartile of ferritin was associated with an increased risk of type 2 diabetes when it was adjusted to BMI and HOMA-IR; this association was independent of the inflammatory status. The highest level of hepcidin gene expression also showed a trend of increased risk of diabetes, however it was not significant. Levels of hsCRP over 2 mg/L showed a significant trend of increasing the risk of diabetes. In conclusion, iron may stimulate the expression of pro-inflammatory genes (TNF-α and IL-6), and both hepcidin and ferritin gene expression levels could be a risk factor for the development of type 2 diabetes. Subjects that have an increased cardiovascular risk also have a major risk to develop type 2 diabetes, which is independent of the BMI and insulin resistance state.

Modelling reactive and proactive behaviour in simulation

This research investigated the simulation model behaviour of a traditional and combined discrete event as well as agent based simulation models when modelling human reactive and proactive behaviour in human centric complex systems. A departmental store was chosen as human centric complex case study where the operation system of a fitting room in WomensWear department was investigated. We have looked at ways to determine the efficiency of new management policies for the fitting room operation through simulating the reactive and proactive behaviour of staff towards customers. Once development of the simulation models and their verification had been done, we carried out a validation experiment in the form of a sensitivity analysis. Subsequently, we executed a statistical analysis where the mixed reactive and proactive behaviour experimental results were compared with some reactive experimental results from previously published works. Generally, this case study discovered that simple proactive individual behaviour could be modelled in both simulation models. In addition, we found the traditional discrete event model performed similar in the simulation model output compared to the combined discrete event and agent based simulation when modelling similar human behaviour.

Enterprise Collaboration Framework for Managing, Advancing and Unifying the Functionality of Multiple Cloud-Based Services with the Help of a Graph API

Part 5: Service Orientation in Collaborative Networks

Hyperlinks in e-books : expanding the functionality of end-notes

With its powerful search engines and billions of published pages, the Worldwide Web has become the ultimate tool to explore the human experience. But, despite the advent of the digital revolution, e-books, at their core, have remained remarkably similar to their printed siblings. This has resulted in a clear dichotomy between two ways of reading: on one side, the multi-dimensional world of the Web; on the other, the linearity of books and e-books. My investigation of the literature indicates that the focus of attempts to merge these two modes of production, and hence of reading, has been the insertion of interactivity into fiction. As I will show in the Literature Review, a clear thrust of research since the early 1990s, and in my opinion the most significant, has concentrated on presenting the reader with choices that affect the plot. This has resulted in interactive stories in which the structure of the narrative can be altered by the reader of experimental fiction. The interest in this area of research is not surprising, as the interaction of readers with the fabric of the narrative provides a fertile ground for exploring, analysing, and discussing issues of plot consistency and continuity. I found in the literature several papers concerned with the effects of hyperlinking on literature, but none about how hyperlinked material and narrative could be integrated without compromising the narrative flow as designed by the author. It led me to think that the researchers had accepted hypertextuality and the linear organisation of fiction as being antithetical, thereby ignoring the possibility of exploiting the first while preserving the second. All the works I consulted were focussed on exploring the possibilities provided to authors (and readers) by hypertext or how hypertext literature affects literary criticism. This was true in earlier works by Landow and Harpold and remained true in later works by Bolter and Grusin. To quote another example, in his book Hypertext 3.0, Landow states: “Most who have speculated on the relation between hypertextuality and fiction concentrate [...] on the effects it will have on linear narrative”, and “hypertext opens major questions about story and plot by apparently doing away with linear organization” (Landow, 2006, pp. 220, 221). In other words, the authors have added narrative elements to Web pages, effectively placing their stories in a subordinate role. By focussing on “opening up” the plots, the researchers have missed the opportunity to maintain the integrity of their stories and use hyperlinked information to provide interactive access to backstory and factual bases. This would represent a missing link between the traditional way of reading, in which the readers have no influence on the path the author has laid out for them, and interactive narrative, in which the readers choose their way across alternatives, thereby, at least to a certain extent, creating their own path. It would be, to continue the metaphor, as if the readers could follow the main path created by the author while being able to get “sidetracked” into exploring hyperlinked material. In Hypertext 3.0, Landow refers to an “Axial structure [of hypertext] characteristic of electronic books and scholarly books with foot-and endnotes” versus a “Network structure of hypertext” (Landow, 2006, p. 70). My research aims at generalising the axial structure and extending it to fiction without losing the linearity at its core. In creative nonfiction, the introduction of places, scenes, and settings, together with characterisation, brings to life the facts without altering them; while much fiction draws on facts to provide a foundation, or narrative elements, for the work. But how can the reader distinguish between facts and representations? For example, to what extent do dialogues and perceptions present what was actually said and thought? Some authors of creative nonfiction use end-notes to provide comments and citations while minimising disruption the flow of the main text, but they are limited in scope and constrained in space. Each reader should be able to enjoy the narrative as if it were a novel but also to explore the facts at the level of detail s/he needs. For this to be possible, end-notes should provide a Web-like way of exploring in more detail what the author has already researched. My research aims to develop ways of integrating narrative prose and hyperlinked documents into a Hyperbook. Its goal is to create a new writing paradigm in which a story incorporates a gateway to detailed information. While creative nonfiction uses the techniques of fictional writing to provide reportage of actual events and fact-based fiction illuminates the affectual dimensions of what happened (e.g., Kate Grenville’s The Secret River and Hilary Mantel’s Wolf Hall), Hyperbooks go one step further and link narrative prose to the details of the events on which the narrative is based or, more in general, to information the reader might find of interest. My dissertation introduces and utilises Hyperbooks to engage in two parallel types of investigation Build knowledge about Italian WWII POWs held in Australia and present it as part of a novella in Hyperbook format. Develop a new piece of technology capable of extending the writing and reading process.

Potential protective role of reactive astrocytes in the periventricular parenchyma in congenital hydrocephalus

Background Cerebrospinal fluid accumulation in hydrocephalus produces an elevation of intraventricular pressure with pathological consequences on the periventricular brain parenchyma including ischemia, oedema, oxidative stress, and accumulation of metabolic waste products. Here we studied in the hyh mouse, an animal model of congenital hydrocephalus, the role of reactive astrocytes in this clinical degenerative condition. Materials and Methods Wild type and hydrocephalic hyh mice at 30 days of postnatal age were used. Three metabolites related to the oxidative and neurotoxic conditions were analysed in ex vivo samples (glutathione, glutamine and taurine) using High Resolution Magic Angle Spinning (HR-MAS). Glutathione synthetase and peroxidase, glutamine synthetase, kidney-type glutaminase (KGA), and taurine/taurine transporter were immunolocated in brain sections. Results Levels of the metabolites were remarkably higher in hydrocephalic conditions. Glutathione peroxidase and synthetase were both detected in the periventricular reactive astrocytes and neurons. Taurine was mostly found free in the periventricular parenchyma and in the reactive astrocytes, and the taurine transporter was mainly present in the neurons located in such regions. Glutamine synthetase was found in reactive astrocytes. Glutaminase was also detected in the reactive astrocytes and in periventricular neurons. These results suggest a possible protective response of reactive astrocytes against oxidative stress and neurotoxic conditions. Conclusions Astrocyte reaction seems to trigger an anti-oxidative and anti-neurotoxic response in order to ameliorate pathological damage in periventricular areas of the hydrocephalic mice.

New insights into plant salt acclimation: the roles of vesicle trafficking and reactive oxygen species signalling in mitochondria and the endomembrane system

In this study, we investigated the cellular and molecular mechanisms that regulate salt acclimation. The main objective was to obtain new insights into the molecular mechanisms that control salt acclimation. Therefore, we carried out a multidisciplinary study using proteomic, transcriptomic, subcellular and physiological techniques. We obtained a Nicotiana tabacum BY-2 cell line acclimated to be grown at 258 mM NaCl as a model for this study. The proteomic and transcriptomic data indicate that the molecular response to stress (chaperones, defence proteins, etc.) is highly induced in these salt-acclimated cells. The subcellular results show that salt induces sodium compartmentalization in the cell vacuoles and seems to be mediated by vesicle trafficking in tobacco salt-acclimated cells. Our results demonstrate that abscisic acid (ABA) and proline metabolism are crucial in the cellular signalling of salt acclimation, probably regulating reactive oxygen species (ROS) production in the mitochondria. ROS may act as a retrograde signal, regulating the cell response. The network of endoplasmic reticulum and Golgi apparatus is highly altered in salt-acclimated cells. The molecular and subcellular analysis suggests that the unfolded protein response is induced in salt-acclimated cells. Finally, we propose that this mechanism may mediate cell death in salt-acclimated cells.