TMAX – a Database System Integrating Tissue Biomarker & Genomic Data

Background: Popular approaches in human tissue-based biomarker discovery include tissue microarrays (TMAs) and DNA Microarrays (DMAs) for protein and gene expression profiling respectively. The data generated by these analytic platforms, together with associated image, clinical and pathological data currently reside on widely different information platforms, making searching and cross-platform analysis difficult. Consequently, there is a strong need to develop a single coherent database capable of correlating all available data types.

Method: This study presents TMAX, a database system to facilitate biomarker discovery tasks. TMAX organises a variety of biomarker discovery-related data into the database. Both TMA and DMA experimental data are integrated in TMAX and connected through common DNA/protein biomarkers. Patient clinical data (including tissue pathological data), computer assisted tissue image and associated analytic data are also included in TMAX to enable the truly high throughput processing of ultra-large digital slides for both TMAs and whole slide tissue digital slides. A comprehensive web front-end was built with embedded XML parser software and predefined SQL queries to enable rapid data exchange in the form of standard XML files.

Results & Conclusion: TMAX represents one of the first attempts to integrate TMA data with public gene expression experiment data. Experiments suggest that TMAX is robust in managing large quantities of data from different sources (clinical, TMA, DMA and image analysis). Its web front-end is user friendly, easy to use, and most importantly allows the rapid and easy data exchange of biomarker discovery related data. In conclusion, TMAX is a robust biomarker discovery data repository and research tool, which opens up the opportunities for biomarker discovery and further integromics research.

Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line

Here, we describe gene expression compositional assignment (GECA), a powerful, yet simple method based on compositional statistics that can validate the transfer of prior knowledge, such as gene lists, into independent data sets, platforms and technologies. Transcriptional profiling has been used to derive gene lists that stratify patients into prognostic molecular subgroups and assess biomarker performance in the pre-clinical setting. Archived public data sets are an invaluable resource for subsequent in silico validation, though their use can lead to data integration issues. We show that GECA can be used without the need for normalising expression levels between data sets and can outperform rank-based correlation methods. To validate GECA, we demonstrate its success in the cross-platform transfer of gene lists in different domains including: bladder cancer staging, tumour site of origin and mislabelled cell lines. We also show its effectiveness in transferring an epithelial ovarian cancer prognostic gene signature across technologies, from a microarray to a next-generation sequencing setting. In a final case study, we predict the tumour site of origin and histopathology of epithelial ovarian cancer cell lines. In particular, we identify and validate the commonly-used cell line OVCAR-5 as non-ovarian, being gastrointestinal in origin. GECA is available as an open-source R package.

Cross-layer Framework for Fine-grained Channel Access in Next Generation High-density WiFi Networks

Densely deployed WiFi networks will play a crucial role in providing the capacity for next generation mobile internet. However, due to increasing interference, overlapped channels in WiFi networks and throughput efficiency degradation, densely deployed WiFi networks is not a guarantee to obtain higher throughput. An emergent challenge is how to efficiently utilize scarce spectrum resources, by matching physical layer resources to traffic demand. In this aspect, access control allocation strategies play a pivotal role but remain too coarse-grained. As a solution, this research proposes a flexible framework for fine-grained channel width adaptation and multi-channel access in WiFi networks. This approach, named SFCA (Sub-carrier Fine-grained Channel Access), adopts DOFDM (Discontinuous Orthogonal Frequency Division Multiplexing) at the PHY layer. It allocates the frequency resource with a sub-carrier granularity, which facilitates the channel width adaptation for multi-channel access and thus brings more flexibility and higher frequency efficiency. The MAC layer uses a frequency-time domain backoff scheme, which combines the popular time-domain BEB scheme with a frequency-domain backoff to decrease access collision, resulting in higher access probability for the contending nodes. SFCA is compared with FICA (an established access scheme) showing significant outperformance. Finally we present results for next generation 802.11ac WiFi networks.

Intentions Toward Physical Activity and Resting Behavior in Pregnant Women: Using the Theory of Planned Behavior Framework in a Cross-Sectional Study

BACKGROUND: Pregnant women are recommended to 1) perform daily moderate-intensity physical activity and 2) limit the amount of sedentary time. Many women do not meet these recommendations. Reduced physical activity and increased sedentary behavior may result from women actively intending to rest during pregnancy. The Theory of Planned Behavior (TPB) has been used to assess attitudes (e.g., positive/negative beliefs), subjective norms (e.g., perception of others' views), perceived behavioral control (PBC) (e.g., self-efficacy), and intention toward exercising while pregnant but has not been applied to aspects pertaining to resting during pregnancy.

METHODS: Pregnant women (n = 345) completed a cross-sectional questionnaire that included two TPB Questionnaires where the target behaviors were 1) being physically active and 2) resting. Bootstrapped paired t tests, ANOVA, and linear hierarchal regression analyses were performed to identify predictors of intentions and whether intentions toward the two behaviors varied at different stages of pregnancy.

RESULTS: As women progressed in their pregnancy, their attitude, PBC, and intention toward being physically active all significantly declined. A positive attitude, subjective norms, and intention toward resting all significantly increased with the advancing trimester. Self-reported health conditions predicted lower intention for physical activity but not for resting.

DISCUSSION: The significantly inverse relationship between physical activity and resting across time suggests that women feel they should focus on one behavior at the expense of the other. Finding that women generally do not perceive these behaviors as mutually compatible has implications in strategizing as to how to encourage women to be active during pregnancy.

Cross-Border Environmental Governance and EC Law

This article examines the nature and scope of emerging cross-border participatory rights under European Community environmental law. It reviews the legal and political forces that have stimulated the development of such rights and also the specific nature of the rights conferred by three major legislative initiatives: the Community Directives on Environmental Impact Assessment, Integrated Pollution Prevention and Control, and the Water Framework Directive. The article concludes with a case study on Ireland which assesses the likely significance of these cross-border participatory rights for transboundary environmental governance in Ireland.

Cross-Kerr-based information transfer processes

The realization of nonclassical states is an important task for many applications of quantum information processing. Usually, properly tailored interactions, different from goal to goal, are considered in order to accomplish specific tasks within the general framework of quantum state engineering. In this paper, we remark on the flexibility of a cross-Kerr nonlinear coupling in hybrid systems as an important ingredient in the engineering of nonclassical states. The general scenario we consider is the implementation of high cross-Kerr nonlinearity in cavity-quantum electrodynamics. In this context, we discuss the possibility of performing entanglement transfer and swapping between matter qubits and light fields initially prepared in separable coherent states. The recently introduced concept of entanglement reciprocation is also considered and shown to be possible with our scheme. We reinterpret some of our results in terms of applications of a generalized Ising interaction to systems of different nature.

A healthy settings framework: an evaluation and comparison of midwives' responses to addressing domestic violence

Objectives: to compare and contrast how midwives working in either hospital- or community-based settings address domestic violence by evaluating their views on: prevalence of domestic violence; their role in addressing domestic violence; the acceptability of routine enquiry; and barriers encountered in asking clients questions about violence and abuse in pregnancy. Design: a postal survey questionnaire. Setting: Northern Ireland. Study population: 983 hospital and community midwives. Findings: overall, 488 midwives returned a completed questionnaire; a 57% response rate. Comparisons were made using descriptive, inferential statistics and cross-tabulation. Although there were significant differences between hospital- and community-based midwives in relation to domestic violence, both groups of midwives tended to underestimate its prevalence. Key conclusions: the findings suggest that midwives per se identify and respond to a fraction of the cases of domestic abuse in pregnancy, due to lack of confidence, education and training. This reinforces the need for both hospital and community midwives to gain further confidence and an understanding of the many psychosocial factors that surround domestic violence. Implications for practice: healthy settings theory can be used effectively to identify good practice with women who experience domestic violence. Effective investment for health care requires the gaps between hospital- and community-based practice to be bridged, and for work to be integrated.

Delivery of Methylene Blue and meso-tetra (N-methyl-4-pyridyl) porphine tetra tosylate from cross-linked poly(vinyl alcohol) hydrogels: A potential means of photodynamic therapy of infected wounds

Poly(vinyl alcohol)-borate complexes were evaluated as a potentially novel drug delivery platform suitable for in vivo use in photodynamic antimicrobial chemotherapy (PACT) of wound infections. An optimised formulation (8.0%w/w PVA, 2.0% w/w borax) was loaded with 1.0 mg ml(-1) of the photosensitisers Methylene Blue (MB) and meso-tetra (N-methyl-4-pyridyl) porphine tetra tosylate (TMP). Both drugs were released to yield receiver compartment concentrations (>5.0 mu g ml(-1)) found to be phototoxic to both planktonic and bicifilm-grown methicillin-resistant Staphylococcus aureus (MRSA), a common cause of wound infections in hospitals. Newborn calf serum, used to simulate the conditions prevalent in an exuding wound, did not adversely affect the properties of the hydrogels and had no significant effect on the rate of TMP-mediated photodynamic kill of MRSA, despite appreciably reducing the fluence rate of incident light. However, MB-mediated photodynamic kill of MRSA was significantly reduced in the presence of calf serum and when the clinical isolate was grown in a biofilm. Results support the contention that delivery of MB or TMP using gel-type vehicles as part of PACT could make a contribution to the photodynamic eradication of MRSA from infected wounds. (C) 2009 Elsevier B.V. All rights reserved.

Folkbiology doesn’t come from Folkpsychology: evidence from Yukatek Maya in cross-cultural perspective

Nearly all psychological research on basic cognitive processes of category formation and reasoning uses sample populations associated with large research institutions in technologically-advanced societies. Lopsided attention to a select participant pool risks biasing interpretation, no matter how large the sample or how statistically reliable the results. The experiments in this article address this limitation. Earlier research with urban-USA children suggests that biological concepts are (1) thoroughly enmeshed with their notions of naive psychology, and (2) strikingly human-centered. Thus, if children are to develop a causally appropriate model of biology, in which humans are seen as simply one animal among many, they must undergo fundamental conceptual change. Such change supposedly occurs between 7 and 10 years of age, when the human-centered view is discarded. The experiments reported here with Yukatek Maya speakers challenge the empirical generality and theoretical importance of these claims. Part 1 shows that young Maya children do not anthropocentrically interpret the biological world. The anthropocentric bias of American children appears to owe to a lack of cultural familiarity with non-human biological kinds, not to initial causal understanding of folkbiology as such. Part 2 shows that by age of 4-5 (the earliest age tested in this regard) Yukatek Maya children employ a concept of innate species potential or underlying essence much as urban American children seem to, namely, as an inferential framework for understanding the affiliation of an organism to a biological species, and for projecting known and unknown biological properties to organisms in the face of uncertainty. Together, these experiments indicate that folkpsychology cannot be the initial source of folkbiology. They also underscore the possibility of a species-wide and domain-specific basis for acquiring knowledge about the living world that is constrained and modified but not caused or created by prior nonbiological thinking and subsequent cultural experience.

Phosphotungstic Acid Encapsulated in Metal-Organic Framework as Catalysts for Carbohydrate Dehydration to 5-Hydroxymethylfurfural

MIL-101, a chromium-based metal-organic framework, is known for its very large pore size, large surface area and good stability. However, applications of this material in catalysis are still limited. 5-Hydroxymethylfurfural (HMF) has been considered a renewable chemical platform for the production of liquid fuels and fine chemicals. Phosphotungstic acid, H3PW12O40 (PTA), encapsulated in MIL-101 is evaluated as a potential catalyst for the selective dehydration of fructose and glucose to 5-hydroxymethylfurfural. The results demonstrate that PTA/MIL-101 is effective for HMF production from fructose in DMSO and can be reused. This is the first example of the application of a metal-organic framework in carbohydrate dehydration.