The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies

Effects of Art from the Heart on Nurse Satisfaction and Patient Well-Being

Introduction. Art programs have been shown to positively affect unit culture, quality of care, and nursing practices. Art interventions improve well-being, reduce stress, and enhance nurse-patient communication. Art from the Heart (AFTH) is an art program that provides art supplies, visual art, and patient About Me pages to patients, families and employees at University of Vermont Medical Center (UVMMC).Objective. Assess the efficacy of AFTH through nursing staff perceptions, understanding, and attitudes toward the program.Methods. Structured interviews were conducted on Baird 4, an adult inpatient ward, at UVMMC. A 19-question survey using Likert scales and short answer formats was administered to nursing staff. Questions assessed perceptions of effects of art on patient anxiety and pain, communication, and job satisfaction. Surveys were analyzed to extract major and minor themes.Results. Twenty-eight interviews were obtained and two major themes emerged: nurse satisfaction and patient well-being. Nursing staff satisfaction minor themes included improved productivity, promoting conversation, and creating a positive influence on the unit. Respondents reported that AFTH helped initiate conversations with patients (100% of respondents) and reduced workday stress (68%). The second major theme, patient well-being, included benefits to patients with dementia, providing comfort, and serving as an outlet or distraction. Utilizing AFTH improved perceived patient mood (100%), health (78.5%), and reduced patient anxiety (89.3%).Conclusions. AFTH provides positive benefits by reducing nursing staff stress and perceived patient anxiety; improving communication, perceived patient mood and health; and creating a sense of community. AFTH should be expanded to the entire 6 Community Agency: Burlington City Arts, Art from the Hearthttps://scholarworks.uvm.edu/comphp_gallery/1240/thumbnail.jp

High-latitude eruptions cast shadow over the African monsoon and the flow of the Nile

Nile River records indicate very low flow following the 1783–1784 Laki volcanic eruption, as well as after other high-latitude volcanic eruptions. As shown by climate model simulations of the Laki eruption, significant cooling (−1° to −3°C) of the Northern Hemisphere land masses during the boreal summer of 1783 resulted in a strong dynamical effect of weakening the African and Indian monsoon circulations, with precipitation anomalies of −1 to −3 mm/day over the Sahel of Africa, thus producing the low Nile flow. Future high-latitude eruptions would significantly impact the food and water supplies in these areas. Using observations of the flow of the Nile River, this new understanding is used to support a date of 939 for the beginning of the eruption of the Eldgjá volcano in Iceland, the largest high-latitude eruption of the past 1500 years

Comparison of CDMS [100] and [111] oriented germanium detectors

The Cryogenic Dark Matter Search (CDMS) utilizes large mass, 3" diameter $\times$ 1" thick target masses as particle detectors. The target is instrumented with both phonon and ionization sensors and comparison of energy in each channel provides event-by-event classification of electron and nuclear recoils. Fiducial volume is determined by the ability to obtain good phonon and ionization signal at a particular location. Due to electronic band structure in germanium, electron mass is described by an anisotropic tensor with heavy mass aligned along the symmetry axis defined by the [111] Miller index (L valley), resulting in large lateral component to the transport. The spatial distribution of electrons varies significantly for detectors which have their longitudinal axis orientations described by either the [100] or [111] Miller indices. Electric fields with large fringing component at high detector radius also affect the spatial distribution of electrons and holes. Both effects are studied in a 3 dimensional Monte Carlo and the impact on fiducial volume is discussed.Comment: Low Temperature Detector 14 conference proceedings to be published in the Journal of Low Temperature Physic

Effect of ethnicity on live birth rates after in vitro fertilisation/intracytoplasmic sperm injection treatment: analysis of UK national database

Objective To evaluate the effect of ethnicity of women on the outcome of in vitro fertilisation (IVF) or intracytoplasmic sperm injection (ICSI) treatment. Design Observational cohort study. Setting UK National Database. Population Data from 2000 to 2010 involving 38 709 women undergoing their first IVF/ICSI cycle were analysed. Methods Anonymous data were obtained from the Human Fertilization and Embryology Authority (HFEA), the statutory regulator of IVF and ICSI treatment in the UK. Data analysis was performed by regression analysis with adjustment for age, cause and type of infertility and treatment type (IVF or ICSI) to express results as odds ratio (OR) and 95% confidence intervals (95% CI). Methods Live birth rate per cycle of IVF or ICSI treatment. Results While white Irish (OR 0.73; 95% CI 0.60–0.90), Indian (0.85; 0.75–0.97), Bangladeshi (0.53: 0.33–0.85), Pakistani (0.68; 0.58–0.80), Black African (0.60; 0.51–0.72), and other non-Caucasian Asian (0.86; 0.73–0.99) had a significantly lower odds of live birth rates per fresh IVF/ICSI cycle than White British women, ethnic groups of White European (1.04; 0.96–1.13), Chinese (1.12; 0.77–1.64), Black Caribbean (0.76; 0.51–1.13), Middle Eastern (0.73; 0.51–1.04), Mediterranean European (1.18; 0.83–1.70) and Mixed race population (0.94; 0.73–1.19) had live birth rates that did not differ significantly. The cumulative live birth rates showed similar patterns across different ethnic groups. Conclusion Ethnicity is a major determinant of IVF/ICSI treatment outcome as indicated by significantly lower live birth rates in some of the ethnic minority groups compared with white British women

The Watchers of the Water

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AGE-modified basement membrane cooperates with Endo180 to promote epithelial cell invasiveness and decrease prostate cancer survival

Biomechanical strain imposed by age-related thickening of the basal lamina and augmented tissue stiffness in the prostate gland coincides with increased cancer risk. Here we hypothesized that the structural alterations in the basal lamina associated with age can induce mechanotransduction pathways in prostate epithelial cells (PECs) to promote invasiveness and cancer progression. To demonstrate this, we developed a 3D model of PEC acini in which thickening and stiffening of basal lamina matrix was induced by advanced glycation end-product (AGE)-dependent non-enzymatic crosslinking of its major components, collagen IV and laminin. We used this model to demonstrate that antibody targeted blockade of CTLD2, the second of eight C-type lectin-like domains in Endo180 (CD280, CLEC13E, KIAA0709, MRC2, TEM9, uPARAP) that can recognize glycosylated collagens, reversed actinomyosin-based contractility [myosin-light chain-2 (MLC2) phosphorylation], loss of cell polarity, loss of cell–cell junctions, luminal infiltration and basal invasion induced by AGE-modified basal lamina matrix in PEC acini. Our in vitro results were concordant with luminal occlusion of acini in the prostate glands of adult Endo180ΔEx2–6/ΔEx2–6 mice, with constitutively exposed CTLD2 and decreased survival of men with early (non-invasive) prostate cancer with high epithelial Endo180 expression and levels of AGE. These findings indicate that AGE-dependent modification of the basal lamina induces invasive behaviour in non-transformed PECs via a molecular mechanism linked to cancer progression. This study provides a rationale for targeting CTLD2 in Endo180 in prostate cancer and other pathologies in which increased basal lamina thickness and tissue stiffness are driving factors

Synaesthesia: a distinct entity that is an emergent feature of adaptive neurocognitive differences

In this article, I argue that synaesthesia is not on a continuum with neurotypical cognition. Synaesthesia is special: its phenomenology is different; it has distinct causal mechanisms; and is likely to be associated with a distinct neurocognitive profile. However, not all synaesthetes are the same, and there are quantifiable differences between them. In particular, the number of types of synaesthesia that a person possesses is a hitherto underappreciated variable that predicts cognitive differences along a number of dimensions (mental imagery, sensory sensitivity, attention to detail). Together with enhanced memory, this may constitute a common core of abilities that may go some way to explaining why synaesthesia might have evolved. I argue that the direct benefits of synaesthesia are generally limited (i.e. the synaesthetic associations do not convey novel information about the world) but, nevertheless, synaesthesia may develop due to other adaptive functions (e.g. perceptual ability, memory) that necessitate changes to design features of the brain. The article concludes by suggesting that synaesthesia forces us to reconsider what we mean by a ‘normal’ mind/brain. There may be multiple ‘normal’ neurodevelopmental trajectories that can sculpt very different ways of experiencing the world, of which synaesthesia is but one. This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’

Organizational and formational structures of networks in the mental lexicon: A State-of-the-art through systematic review

This state-of-the-art presents a systematic exploration on the use of network patterns in global research efforts to understand, organize and represent the mental lexicon. Results have shown an increase over recent years in the usage of complex, small-world and scale-free network patterns within the literature.With the increasing complexity of network patterns, we see more potential in the inter-disciplinary exploration of the mental lexicon through universal and mathematically-describable, behavioral patterns in small-world and scale-free networks. A systematic review of 36 items of methodologically-selected literature serve as a means to explore how the greater literary body understands network structures within the mental lexicon. Network-based approaches are discriminated between three contrasting varieties. These include: 'simple networks', characterized by arbitrarily organized graph patterns of metaphorical importance; 'connectionist networks', a broad category of networks which explore the structural features of a system through the analysis of emergent properties; and lastly 'complex networks', distinguished as small-world, scale-free networks which follow a strict and mathematically-describable structure in agreement with the Barabási-Albert model. Each network approach is explored in terms of their discernible di erences which relate to their parameters and affect their implications. A final evaluation of observed patterns within the selected literature is o ered, as well as an elaboration on the sense of trajectory beheld in the research in order to offer insight and orientation for future research