Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2?kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatellite-inducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.

Wind generation output during cold weather-driven electricity demand peaks in Ireland

Recent cold winters and prolonged periods of low wind speeds have prompted concerns about the increasing penetration of wind generation in the Irish and other northern European power systems. On the combined Republic of Ireland and Northern Ireland system there was in excess of 1.5 GW of installed wind power in January 2010. As the penetration of these variable, non-dispatchable generators increases, power systems are becoming more sensitive to weather events on the supply side as well as on the demand side. In the temperate climate of Ireland, sensitivity of supply to weather is mainly due to wind variability while demand sensitivity is driven by space heating or cooling loads. The interplay of these two weather-driven effects is of particular concern if demand spikes driven by low temperatures coincide with periods of low winds. In December 2009 and January 2010 Ireland experienced a prolonged spell of unusually cold conditions. During much of this time, wind generation output was low due to low wind speeds. The impacts of this event are presented as a case study of the effects of weather extremes on power systems with high penetrations of variable renewable generation.

Bio-port Free Energy City

In an age of depleting oil reserves and increasing energy demand, humanity faces a stalemate between environmentalism and politics, where crude oil is traded at record highs yet the spotlight on being ‘green’ and sustainable is stronger than ever. A key theme on today’s political agenda is energy independence from foreign nations, and the United Kingdom is bracing itself for nuclear renaissance which is hoped will feed the rapacious centralised system that the UK is structured upon. But what if this centralised system was dissembled, and in its place stood dozens of cities which grow and monopolise from their own energy? Rather than one dominant network, would a series of autonomous city-based energy systems not offer a mutually profitable alternative? Bio-Port is a utopian vision of a ‘Free Energy City’ set in Liverpool, where the old dockyards, redundant space, and the Mersey Estuary have been transformed into bio-productive algae farms. Bio-Port Free Energy City is a utopian ideal, where energy is superfluous; in fact so abundant that meters are obsolete. The city functions as an energy generator and thrives from its own product with minimal impact upon the planet it inhabits. Algaculture is the fundamental energy source, where a matrix of algae reactors swamp the abandoned dockyards; which themselves have been further expanded and reclaimed from the River Mersey. Each year, the algae farm is capable of producing over 200 million gallons of bio-fuel, which in-turn can produce enough electricity to power almost 2 million homes. The metabolism of Free-Energy City is circular and holistic, where the waste products of one process are simply the inputs of a new one. Livestock farming – once traditionally a high-carbon countryside exercise has become urbanised. Cattle are located alongside the algae matrix, and waste gases emitted by farmyards and livestock are largely sequestered by algal blooms or anaerobically converted to natural gas. Bio-Port Free Energy City mitigates the imbalances between ecology and urbanity, and exemplifies an environment where nature and the human machine can function productively and in harmony with one another. According to James Lovelock, our population has grown in number to the point where our presence is perceptibly disabling the planet, but in order to reverse the effects of our humanist flaws, it is vital that new eco-urban utopias are realised.

Inactivation of Rb in stromal fibroblasts promotes epithelial cell invasion

Stromal-derived growth factors are required for normal epithelial growth but are also implicated in tumour progression. We have observed inactivation of the retinoblastoma protein (Rb), through phosphorylation, in cancer-associated fibroblasts in oro-pharyngeal cancer specimens. Rb is well known for its cell-autonomous effects on cancer initiation and progression; however, cell non-autonomous functions of Rb are not well described. We have identified a cell non-autonomous role of Rb, using three-dimensional cultures, where depletion of Rb in stromal fibroblasts enhances invasive potential of transformed epithelia. In part, this is mediated by upregulation of keratinocyte growth factor (KGF), which is produced by the depleted fibroblasts. KGF drives invasion of epithelial cells through induction of MMP1 expression in an AKT- and Ets2-dependent manner. Our data identify that stromal fibroblasts can alter the invasive behaviour of the epithelium, and we show that altered expression of KGF can mediate these functions. © European Molecular Biology Organization.

Scalable black-box prediction models for multi-dimensional adaptation on NUMA multi-cores

This paper presents a scalable, statistical ‘black-box’ model for predicting the performance of parallel programs on multi-core non-uniform memory access (NUMA) systems. We derive a model with low overhead, by reducing data collection and model training time. The model can accurately predict the behaviour of parallel applications in response to changes in their concurrency, thread layout on NUMA nodes, and core voltage and frequency. We present a framework that applies the model to achieve significant energy and energy-delay-square (ED2) savings (9% and 25%, respectively) along with performance improvement (10% mean) on an actual 16-core NUMA system running realistic application workloads. Our prediction model proves substantially more accurate than previous efforts.

Wind generation and electricity demand during the severe winter of 2009/10 in Ireland

Throughout the world the share of wind power in the generation mix is increasing. In the All Island Grid, of the Republic of Ireland and Northern Ireland there is now over 1.5 GW of installed wind power. As the penetration of these variable, non-dispatchable generators increases, power systems are becoming more sensitive to weather events on the supply side as well as on the demand side. In the temperate climate of Ireland, sensitivity of supply to weather is mainly due to wind variability while demand sensitivity is driven by space heating or cooling loads. The interplay of these two weather-driven effects is of particular concern if demand spikes driven by low temperatures coincide with periods of low winds. In December 2009 and January 2010 Ireland experienced a prolonged spell of unusually cold conditions. During much of this time, wind generation output was low due to low wind speeds. The impacts of this event are presented as a case study of the effects of weather extremes on power systems with high penetrations of variable renewable generation.

PAMOP: Petascale atomic, molecular and optical collision calculations

Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schr\"odinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. In this report, various examples are shown from our theoretical results compared with experimental results obtained from Synchrotron Radiation facilities where the Cray architecture at HLRS is playing an integral part in our computational projects.

Work Extraction and Energy Storage in the Dicke Model

We study work extraction from the Dicke model achieved using simple unitary cyclic transformations keeping into account both a non optimal unitary protocol, and the energetic cost of creating the initial state. By analyzing the role of entanglement, we find that highly entangled states can be inefficient for energy storage when considering the energetic cost of creating the state. Such surprising result holds notwithstanding the fact that the criticality of the model at hand can sensibly improve the extraction of work. While showing the advantages of using a many-body system for work extraction, our results demonstrate that entanglement is not necessarily advantageous for energy storage purposes, when non optimal processes are considered. Our work shows the importance of better understanding the complex interconnections between non-equilibrium thermodynamics of quantum systems and correlations among their subparts.

Stability of 5-aminolevulinic acid in novel non-aqueous gel and patch-type systems intended for topical application.

Aminolevulinic acid (ALA) stability within topical formulations intended for photodynamic therapy (PDT) is poor due to dimerisation to pyrazine-2,5-dipropionic acid (PY). Most strategies to improve stability use low pH vehicles, which can cause cutaneous irritancy. To overcome this problem, a novel approach is investigated that uses a non-aqueous vehicle to retard proton-induced charge separation across the 4-carbonyl group on ALA and lessen nucleophilic attack that leads to condensation dimerisation. Bioadhesive anhydrous vehicles based on methylvinylether-maleic anhydride copolymer patches and poly(ethyleneglycol) or glycerol thickened poly(acrylic acid) gels were formulated. ALA stability fell below pharmaceutically acceptable levels after 6 months, with bioadhesive patches stored at 5°C demonstrating the best stability by maintaining 86.2% of their original loading. Glycerol-based gels maintained 40.2% in similar conditions. However, ALA loss did not correspond to expected increases in PY, indicating the presence of another degradative process that prevented dimerisation. Nuclear magnetic resonance (NMR) analysis was inconclusive in respect of the mechanism observed in the patch system, but showed clearly that an esterification reaction involving ALA and both glycerol and poly(ethyleneglycol) was occurring. This was especially marked in the glycerol gels, where only 2.21% of the total expected PY was detected after 204 days at 5°C. Non-specific esterase hydrolysis demonstrated that ALA was recoverable from the gel systems, further supporting esterified binding within the gel matrices. It is conceivable that skin esterases could duplicate this finding upon topical application of the gel and convert these derivatives back to ALA in situ, provided skin penetration is not affected adversely.

Sequentially continuous non-linear fundamental systems of solutions of affine equations in locally convex spaces

According to the Mickael's selection theorem any surjective continuous linear operator from one Fr\'echet space onto another has a continuous (not necessarily linear) right inverse. Using this theorem Herzog and Lemmert proved that if $E$ is a Fr\'echet space and $T:E\to E$ is a continuous linear operator such that the Cauchy problem $\dot x=Tx$, $x(0)=x_0$ is solvable in $[0,1]$ for any $x_0\in E$, then for any $f\in C([0,1],E)$, there exists a continuos map $S:[0,1]\times E\to E$, $(t,x)\mapsto S_tx$ such that for any $x_0\in E$, the function $x(t)=S_tx_0$ is a solution of the Cauchy problem $\dot x(t)=Tx(t)+f(t)$, $x(0)=x_0$ (they call $S$ a fundamental system of solutions of the equation $\dot x=Tx+f$). We prove the same theorem, replacing "continuous" by "sequentially continuous" for locally convex spaces from a class which contains strict inductive limits of Fr\'echet spaces and strong duals of Fr\'echet--Schwarz spaces and is closed with respect to finite products and sequentially closed subspaces. The key-point of the proof is an extension of the theorem on existence of a sequentially continuous right inverse of any surjective sequentially continuous linear operator to some class of non-metrizable locally convex spaces.

Statistical-based monitoring of multivariate non-Gaussian systems

The monitoring of multivariate systems that exhibit non-Gaussian behavior is addressed. Existing work advocates the use of independent component analysis (ICA) to extract the underlying non-Gaussian data structure. Since some of the source signals may be Gaussian, the use of principal component analysis (PCA) is proposed to capture the Gaussian and non-Gaussian source signals. A subsequent application of ICA then allows the extraction of non-Gaussian components from the retained principal components (PCs). A further contribution is the utilization of a support vector data description to determine a confidence limit for the non-Gaussian components. Finally, a statistical test is developed for determining how many non-Gaussian components are encapsulated within the retained PCs, and associated monitoring statistics are defined. The utility of the proposed scheme is demonstrated by a simulation example, and the analysis of recorded data from an industrial melter.

Building Autonomous Sensitive Artificial Listeners

This paper describes a substantial effort to build a real-time interactive multimodal dialogue system with a focus on emotional and non-verbal interaction capabilities. The work is motivated by the aim to provide technology with competences in perceiving and producing the emotional and non-verbal behaviours required to sustain a conversational dialogue. We present the Sensitive Artificial Listener (SAL) scenario as a setting which seems particularly suited for the study of emotional and non- verbal behaviour, since it requires only very limited verbal understanding on the part of the machine. This scenario allows us to concentrate on non-verbal capabilities without having to address at the same time the challenges of spoken language understanding, task modeling etc. We first report on three prototype versions of the SAL scenario, in which the behaviour of the Sensitive Artificial Listener characters was determined by a human operator. These prototypes served the purpose of verifying the effectiveness of the SAL scenario and allowed us to collect data required for building system components for analysing and synthesising the respective behaviours. We then describe the fully autonomous integrated real-time system we created, which combines incremental analysis of user behaviour, dialogue management, and synthesis of speaker and listener behaviour of a SAL character displayed as a virtual agent. We discuss principles that should underlie the evaluation of SAL-type systems. Since the system is designed for modularity and reuse, and since it is publicly available, the SAL system has potential as a joint research tool in the affective computing research community.