Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells

The retinal vascular endothelium is essential for angiogenesis and is involved in maintaining barrier selectivity and vascular tone. The aim of this study was to identify and quantify microRNAs and other small regulatory non-coding RNAs (ncRNAs) which may regulate these crucial functions. Primary bovine retinal microvascular endothelial cells (RMECs) provide a well-characterized in vitro system for studying angiogenesis. RNA extracted from RMECs was used to prepare a small RNA library for deep sequencing (Illumina Genome Analyzer). A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). In many cases, the most frequent isomiR differed from the sequence reported in miRBase. In addition, five novel microRNAs, 13 novel bovine orthologs of known human microRNAs and multiple new members of the miR-2284/2285 family were detected. Several similar to 30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one-third of all mapped reads. Inhibition of miR-21 with an LNA inhibitor significantly reduced proliferation, migration, and tube-forming capacity of RMECs. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Knockdown of miR-21 suggests a role for this microRNA in regulation of angiogenesis in the retinal microvasculature. J. Cell. Biochem. 113: 20982111, 2012. (C) 2012 Wiley Periodicals, Inc.

A micromechanics approach for damage modeling of polymer matrix composites

A new model for damage evolution in polymer matrix composites is presented. The model is based on a combination of two constituent-level models and an interphase model. This approach reduces the number of empirical parameters since the two constituent- level models are formulated for isotropic materials, namely fiber and matrix. Decomposition of the state variables down to the micro-scale is accomplished by micromechanics. Phenomenological damage evolution models are then postulated for each constituent. Determination of material parameters is made from available experimental data. The required experimental data can be obtained with standard tests. Comparison between model predictions and additional experimental data is presented.

Multiple Luminaire Identification in Airborne Images of Airport’s Approach Lighting Using Mathematical Morphology With Variable Length Structuring Element

The increasing demand for fast air transportation around the clock
has increased the number of night flights in civil aviation over
the past few decades. In night aviation, to land an aircraft, a
pilot needs to be able to identify an airport. The approach
lighting system (ALS) at an airport is used to provide
identification and guidance to pilots from a distance. ALS
consists of more than $100$ luminaires which are installed in a
defined pattern following strict guidelines by the International
Civil Aviation Organization (ICAO). ICAO also has strict
regulations for maintaining the performance level of the
luminaires. However, once installed, to date there is no automated
technique by which to monitor the performance of the lighting. We
suggest using images of the lighting pattern captured using a camera
placed inside an aircraft. Based on the information contained
within these images, the performance of the luminaires has to be
evaluated which requires identification of over $100$ luminaires
within the pattern of ALS image. This research proposes analysis
of the pattern using morphology filters which use a variable
length structuring element (VLSE). The dimension of the VLSE changes
continuously within an image and varies for different images.
A novel
technique for automatic determination of the VLSE is proposed and
it allows successful identification of the luminaires from the
image data as verified through the use of simulated and real data.

Core-based Methodology: An Automated Approach for Implementing a Complete System From Algorithms to a Heterogeneous Network Including FPGAs

In this paper, we present a methodology for implementing a complete Digital Signal Processing (DSP) system onto a heterogeneous network including Field Programmable Gate Arrays (FPGAs) automatically. The methodology aims to allow design refinement and real time verification at the system level. The DSP application is constructed in the form of a Data Flow Graph (DFG) which provides an entry point to the methodology. The netlist for parts that are mapped onto the FPGA(s) together with the corresponding software and hardware Application Protocol Interface (API) are also generated. Using a set of case studies, we demonstrate that the design and development time can be significantly reduced using the methodology developed.

Determining trophic niche width: An experimental test of the stable isotope approach

Determining the trophic niche width of an animal population and the relative degree to which a generalist population consists of dietary specialists are long-standing problems of ecology. It has been proposed that the variance of stable isotope values in consumer tissues could be used to quantify trophic niche width of consumer populations. However, this promising idea has not yet been rigorously tested. By conducting controlled laboratory experiments using model consumer populations (Daphnia sp., Crustacea) with controlled diets, we investigated the effect of individual- and population-level specialisation and generalism on consumer d C mean and variance values. While our experimental data follow general expectations, we extend current qualitative models to quantitative predictions of the dependence of isotopic variance on dietary correlation time, a measure for the typical time over which a consumer changes its diet. This quantitative approach allows us to pinpoint possible procedural pitfalls and critical sources of measurement uncertainty. Our results show that the stable isotope approach represents a powerful method for estimating trophic niche widths, especially when taking the quantitative concept of dietary correlation time into account. © 2012 The Authors.

Isolation of epithelial stem cells from dermis by a three-dimensional culture system

Skin is a representative self-renewing tissue containing stem cells. Although many attempts have been made to define and isolate skin-derived stem cells, establishment of a simple and reliable isolation procedure remains a goal to be achieved. Here, we report the isolation of cells having stem cell properties from mouse embryonic skin using a simple selection method based on an assumption that stem cells may grow in an anchorage-independent manner. We inoculated single cell suspensions prepared from mouse embryonic dermis into a temperature-sensitive gel and propagated the resulting colonies in a monolayer culture. The cells named dermis-derived epithelial progenitor-1 (DEEP) showed epithelial morphology and grew rapidly to a more than 200 population doubling level over a period of 250 days. When the cells were kept confluent, they spontaneously formed spheroids and continuously grew even in spheroids. Immunostaining revealed that all of the clones were positive for the expression of cytokeratin-8, -18, -19, and E-cadherin and negative for the expression of cytokeratin-1, -5, -6, -14, -20, vimentin, nestin, a ckit. Furthermore, they expressed epithelial stem cell markers such as p63, integrin beta1, and S100A6. On exposure to TGFbeta in culture, some of DEEP-1 cells expressed alpha-smooth muscle actin. When the cells were transplanted into various organs of adult SCID mice, a part of the inoculated cell population acquired neural, hepatic, and renal cell properties. These results indicate that the cells we isolated were of epithelial stem cell origin and that our new approach is useful for isolation of multipotent stem cells from skin tissues.

Use of data dependence graphs in the design of bit-level systolic arrays

The use of bit-level systolic array circuits as building blocks in the construction of larger word-level systolic systems is investigated. It is shown that the overall structure and detailed timing of such systems may be derived quite simply using the dependence graph and cut-set procedure developed by S. Y. Kung (1988). This provides an attractive and intuitive approach to the bit-level design of many VLSI signal processing components. The technique can be applied to ripple-through and partly pipelined circuits as well as fully systolic designs. It therefore provides a means of examining the relative tradeoff between levels of pipelining, chip area, power consumption, and throughput rate within a given VLSI design.

Optimized bit level architectures for IIR filtering

Optimized circuits for implementing high-performance bit-parallel IIR filters are presented. Circuits constructed mainly from simple carry save adders and based on most-significant-bit (MSB) first arithmetic are described. Two methods resulting in systems which are 100% efficient in that they are capable of sampling data every cycle are presented. In the first approach the basic circuit is modified so that the level of pipelining used is compatible with the small, but fixed, latency associated with the computation in question. This is achieved through insertion of pipeline delays (half latches) on every second row of cells. This produces an area-efficient solution in which the throughput rate is determined by a critical path of 76 gate delays. A second approach combines the MSB first arithmetic methods with the scattered look-ahead methods. Important design issues are addressed, including wordlength truncation, overflow detection, and saturation.

Current-induced atomic dynamics, instabilities, and Raman signals: Quasiclassical Langevin equation approach

We derive and employ a semiclassical Langevin equation obtained from path integrals to describe the ionic dynamics of a molecular junction in the presence of electrical current. The electronic environment serves as an effective nonequilibrium bath. The bath results in random forces describing Joule heating, current-induced forces including the nonconservative wind force, dissipative frictional forces, and an effective Lorentz-type force due to the Berry phase of the nonequilibrium electrons. Using a generic two-level molecular model, we highlight the importance of both current-induced forces and Joule heating for the stability of the system. We compare the impact of the different forces, and the wide-band approximation for the electronic structure on our result. We examine the current-induced instabilities (excitation of runaway "waterwheel" modes) and investigate the signature of these in the Raman signals.

Assessing pain in preterm infants in the neonatal intensive care unit:moving to a 'brain-oriented' approach

Preterm infants in the neonatal intensive care unit undergo repeated exposure to procedural and ongoing pain. Early and long-term changes in pain processing, stress-response systems and development may result from cumulative early pain exposure. So that appropriate treatment can be given, accurate assessment of pain is vital, but is also complex because these infants' responses may differ from those of full-term infants. A variety of uni- and multidimensional assessment tools are available; however, many have incomplete psychometric testing and may not incorporate developmentally important cues. Near-infrared spectroscopy and/or EEG techniques that measure neonatal pain responses at a cortical level offer new opportunities to validate neonatal pain assessment tools.

Patterns of Holocene relative sea level change in the North of Britain and Ireland

Temporal and spatial patterns of relative sea level (RSL) change in the North of Britain and Ireland during the Holocene are examined. Four episodes, each defined by marked changes in the RSL trend, are identified. Each episode is marked by a rise to a culminating shoreline followed by a fall. Episode HRSL-1 dates from the Younger Dryas to early in the Holocene; HRSL-2 to HRSL-4 occurred later in the Holocene. There is extensive evidence for each episode, and on this basis the spatial distribution of the altitude data for three culminating shorelines and a shoreline formed at the time of the Holocene Storegga Slide tsunami (ca 8110 ± 100 cal. BP) is analysed. Ordinary Kriging is used to determine the general pattern, following which Gaussian Trend Surface Analysis is employed. Recognising that empirical measurements of RSL change can be unevenly distributed spatially, a new approach is introduced which enables the developing pattern to be identified. The patterns for the most widely occurring shorelines were analysed and found to be similar and common centre and axis models were developed for all shorelines. The analyses described provide models of the spatial pattern of Holocene RSL change in the area between ca 8100 cal. BP and ca 1000 cal. BP based on 2262 high resolution shoreline altitude measurements. These models fit the data closely, no shoreline altitude measurement lying more than −1.70 m or +1.82 m from the predicted value. The models disclose a similar pattern to a recently published Glacial Isostatic Adjustment model for present RSL change across the area, indicating that the overall spatial pattern of RSL change may not have varied greatly during the last ca 8000 years.

Visually extracting data records from the deep web

Web sites that rely on databases for their content are now ubiquitous. Query result pages are dynamically generated from these databases in response to user-submitted queries. Automatically extracting structured data from query result pages is a challenging problem, as the structure of the data is not explicitly represented. While humans have shown good intuition in visually understanding data records on a query result page as displayed by a web browser, no existing approach to data record extraction has made full use of this intuition. We propose a novel approach, in which we make use of the common sources of evidence that humans use to understand data records on a displayed query result page. These include structural regularity, and visual and content similarity between data records displayed on a query result page. Based on these observations we propose new techniques that can identify each data record individually, while ignoring noise items, such as navigation bars and adverts. We have implemented these techniques in a software prototype, rExtractor, and tested it using two datasets. Our experimental results show that our approach achieves significantly higher accuracy than previous approaches. Furthermore, it establishes the case for use of vision-based algorithms in the context of data extraction from web sites.

Advancing impact prediction and hypothesis testing in invasion ecology using a comparative functional response approach

Invasion ecology urgently requires predictive methodologies that can forecast the ecological impacts of existing, emerging and potential invasive species. We argue that many ecologically damaging invaders are characterised by their more efficient use of resources. Consequently, comparison of the classical ‘functional response’ (relationship between resource use and availability) between invasive and trophically analogous native species may allow prediction of invader ecological impact. We review the utility of species trait comparisons and the history and context of the use of functional responses in invasion ecology, then present our framework for the use of comparative functional responses. We show that functional response analyses, by describing the resource use of species over a range of resource availabilities, avoids many pitfalls of ‘snapshot’ assessments of resource use. Our framework demonstrates how comparisons of invader and native functional responses, within and between Type II and III functional responses, allow testing of the likely population-level outcomes of invasions for affected species. Furthermore, we describe how recent studies support the predictive capacity of this method; for example, the invasive ‘bloody red shrimp’ Hemimysis anomala shows higher Type II functional responses than native mysids and this corroborates, and could have predicted, actual invader impacts in the field. The comparative functional response method can also be used to examine differences in the impact of two or more invaders, two or more populations of the same invader, and the abiotic (e.g. temperature) and biotic (e.g. parasitism) context-dependencies of invader impacts. Our framework may also address the previous lack of rigour in testing major hypotheses in invasion ecology, such as the ‘enemy release’ and ‘biotic resistance’ hypotheses, as our approach explicitly considers demographic consequences for impacted resources, such as native and invasive prey species. We also identify potential challenges in the application of comparative functional responses in invasion ecology. These include incorporation of numerical responses, multiple predator effects and trait-mediated indirect interactions, replacement versus non-replacement study designs and the inclusion of functional responses in risk assessment frameworks. In future, the generation of sufficient case studies for a meta-analysis could test the overall hypothesis that comparative functional responses can indeed predict invasive species impacts.

Family, state, class and solidarity: re-conceptualising intergenerational solidarity through the grounded theory approach

The relationship between class and intergenerational solidarities in the public and private spheres calls for further conceptual and theoretical development. This article discusses the findings from the first wave of a qualitative longitudinal study entitled Changing Generations, conducted in Ireland in 2011–2012, comprising 100 in-depth interviews with men and women across the age and socioeconomic spectrums. Constructivist grounded theory analysis of the data gives rise to the following postulates: (1) intergenerational solidarity at the family level is strongly contoured by socioeconomic status (SES); (2) intergenerational solidarity evolves as family generations observe each others’ practices and adjust their expectations accordingly; (3) intergenerational solidarity within families is also shaped by the public sphere (the welfare state) that generates varying expectations and levels of solidarity regarding State supports for different age groups, again largely dependent on SES; (4) the liberal welfare state context, especially at a time of economic crisis, enhances the significance of intergenerational solidarity within families. We conclude by calling for research that is attuned to age/generation, gender and class, and how these operate across the family and societal levels.

Community Engagement in Ireland's Developmental Welfare State: a study of the life cycle approach

The idea that people matter in modern democracies, often referred to as 'civic engagement' is recognised at the highest international level (United Nations 2008: 9). Civic or community engagement is essential to how budgets are decided, policy is developed and public services delivered. Significantly, community engagement is crucial in developing policy for sustained economic and social development. In Ireland the idea of the Developmental Welfare State (DWS) is based on the premise that the social policy system should support citizens so as to reach their full potential. Such a system comprises three overlapping elements: tax and welfare transfer, the provision of services and activist initiatives (National Economic and Social Council, 2005: ix-xviii). Civil Society Organisations have been challenged to 'operationalise the DWS' using a 'life cycle framework' as part of Ireland's corporatist partnership model (Department of Taoiseach, 2006: 40).