Global down-regulation of HOX gene expression in PML-RARalpha + acute promyelocytic leukemia identified by small-array real-time PCR

Acute promyelocytic leukemia (APL) is associated with a reciprocal and balanced translocation involving the retinoic acid receptor-alpha (RARalpha). All-trans retinoic acid (ATRA) is used to treat APL and is a potent morphogen that regulates HOX gene expression in embryogenesis and organogenesis. HOX genes are also involved in hematopoiesis and leukemogenesis. Thirty-nine mammalian HOX genes have been identified and classified into 13 paralogous groups clustered on 4 chromosomes. They encode a complex network of transcription regulatory proteins whose precise targets remain poorly understood. The overall function of the network appears to be dictated by gene dosage. To investigate the mechanisms involved in HOX gene regulation in hematopoiesis and leukemogenesis by precise measurement of individual HOX genes, a small-array real-time HOX (SMART-HOX) quantitative polymerase chain reaction (PCR) platform was designed and validated. Application of SMART-HOX to 16 APL bone marrow samples revealed a global down-regulation of 26 HOX genes compared with normal controls. HOX gene expression was also altered during differentiation induced by ATRA in the PML-RARalpha(+) NB4 cell line. PML-RARalpha fusion proteins have been reported to act as part of a repressor complex during myeloid cell differentiation, and a model linking HOX gene expression to this PML-RARalpha repressor complex is now proposed.

Long-range synchronization and local desynchronization of alpha oscillations during visual short-term memory retention in children

Local alpha-band synchronization has been associated with both cortical idling and active inhibition. Recent evidence, however, suggests that long-range alpha synchronization increases functional coupling between cortical regions. We demonstrate increased long-range alpha and beta band phase synchronization during short-term memory retention in children 6-10 years of age. Furthermore, whereas alpha-band synchronization between posterior cortex and other regions is increased during retention, local alpha-band synchronization over posterior cortex is reduced. This constitutes a functional dissociation for alpha synchronization across local and long-range cortical scales. We interpret long-range synchronization as reflecting functional integration within a network of frontal and visual cortical regions. Local desynchronization of alpha rhythms over posterior cortex, conversely, likely arises because of increased engagement of visual cortex during retention.

Optimizing Research on End-of-Life Care for Seniors:The Collective New Emerging Team on End of Life Care for Seniors University of Ottawa, Institute of Palliative Care

Background: End-of-life care for seniors is an important and neglected area of research. The University of Ottawa Institute of Palliative Care has expanded its research capacity by developing a Canadian Institutes of Health Research (CIHR) funded new emerging team on end-of-life care for seniors. This initiative brings together an interdisciplinary team of researchers from palliative care and geriatrics to develop a comprehensive program of research. Methods: 1) A variety of investigators from the fields of palliative care and geriatrics and disciplines of epidemiology, medicine, nursing, psychology and social work will collaborate on the development of a research agenda focussed on end-of-life care for seniors. 2) The conceptual model for the research program consists of 4 broad interrelated domains that are congruent with the CIHR themes of health services, clinical issues, population health and psychosocial, cultural, spiritual and ethical issues; this framework will guide the research program and all studies emanating from the program. 3) Research studies will focus on 5 areas of inquiry that are central to end-of-life care for seniors: palliative end-of-life care for rural seniors, care settings, burden, role of volunteers, and delirium. Results: This new team has the potential to obtain peer-reviewed funding, recruit and train a new generation of researchers, and build a network of concerned researchers. Conclusions: The new team should ultimately contribute to an improved quality of care for seniors who are approaching death.

Surface Energy and Surface Proton Order of Ice Ih

Ice Ih is comprised of orientationally disordered water molecules giving rise to positional disorder of the hydrogen atoms in the hydrogen bonded network of the lattice. Here we arrive at a first principles determination of the surface energy of ice Ih and suggest that the surface of ice is significantly more proton ordered than the bulk. We predict that the proton order-disorder transition, which occurs in the bulk at similar to 72 K, will not occur at the surface at any temperature below surface melting. An order parameter which defines the surface energy of ice Ih surfaces is also identified.

Simulations of Biased Agonists in the β2 Adrenergic Receptor with Accelerated Molecular Dynamics

The biased agonism of the G protein-coupled receptors (GPCRs), where in addition to a traditional G protein-signalling pathway a GPCR promotes intracellular signals though ß-arrestin, is a novel paradigm in pharmacology. Biochemical and biophysical studies have suggested that a GPCR forms a distinct ensemble of conformations signalling through the G protein and ß-arrestin. Here we report on the dynamics of the ß2 adrenergic receptor bound to the ß-arrestin and G protein biased agonists and the empty receptor to further characterize the receptor conformational changes caused by biased agonists. We use conventional and accelerated molecular dynamics (aMD) simulations to explore the conformational transitions of the GPCR from the active state to the inactive state. We found that aMD simulations enable monitoring the transition within the nanosecond timescale while capturing the known microscopic characteristics of the inactive states, such as the ionic lock, the inward position of F6.44, and water clusters. Distinct conformational states are shown to be stabilized by each biased agonist. In particular, in simulations of the receptor with the ß-arrestin biased agonist, N-cyclopentylbutanepherine we observe a different pattern of motions in helix 7 when compared to simulations with the G protein biased agonist, Salbutamol that involves perturbations of the network of interactions within the NPxxY motif. Understanding the network of interactions induced by biased ligands and the subsequent receptor conformational shifts will lead to development of more efficient drugs. © 2013 American Chemical Society

Cinematic Peripheries of Dublin

The term periphery is, most of the time, used with or in relation to the centre. The ‘zoning’ taken by granted by the architect is unlike the one portrayed by the director who frames the differences of places in a non-linear manner. Film offers a constructed urban experience, suggesting the city to be a local network composed of nodes and links, rather than a centre and the margin. It is possible to talk about the construction of a new kind of network in film through a temporal representation of space, of the distant as the close. In this way, film may be a tool to shift the gaze from the bird’s-eye view to the eye level to create ‘a unified perceptual image of the city’, in Christine Boyer’s words. The experienced surface of the city is two-dimensional neither in fiction nor in reality. In this chapter, the nodes of Dublin are examined through two Irish films, Goldfish Memory (Elizabeth Gill, 2003) and Adam and Paul (Leonard Abrahamson, 2004). Specific elements of the city of Dublin, including walls, houses, pubs, streets, bridges, and parks, are analysed to understand the nature of the network of the city composed of nodes and their connections.

Formal calibration methodology for CFD models of naturally ventilated indoor environments

Well planned natural ventilation strategies and systems in the built environments may provide healthy and comfortable indoor conditions, while contributing to a significant reduction in the energy consumed by buildings. Computational Fluid Dynamics (CFD) is particularly suited for modelling indoor conditions in naturally ventilated spaces, which are difficult to predict using other types of building simulation tools. Hence, accurate and reliable CFD models of naturally ventilated indoor spaces are necessary to support the effective design and operation of indoor environments in buildings. This paper presents a formal calibration methodology for the development of CFD models of naturally ventilated indoor environments. The methodology explains how to qualitatively and quantitatively verify and validate CFD models, including parametric analysis utilising the response surface technique to support a robust calibration process. The proposed methodology is demonstrated on a naturally ventilated study zone in the library building at the National University of Ireland in Galway. The calibration process is supported by the on-site measurements performed in a normally operating building. The measurement of outdoor weather data provided boundary conditions for the CFD model, while a network of wireless sensors supplied air speeds and air temperatures inside the room for the model calibration. The concepts and techniques developed here will enhance the process of achieving reliable CFD models that represent indoor spaces and provide new and valuable information for estimating the effect of the boundary conditions on the CFD model results in indoor environments. © 2012 Elsevier Ltd.

Synthesis and characterization of polymer networks and star polymers containing a novel, hydrolyzable acetal-based dimethacrylate cross-linker

An acid-labile dimethaerylate acetal cross-linker,di(methacryloyloxy-l-ethoxy)methane(DMOEM), was synthesized by the reaction of 2-hydroxyethyl methacrylate and paraformaldehyde using p-toluenesulfonic acid and toluene as catalyst and solvent, respectively. Group transfer polymerization was employed to use this cross-linker in the preparation of nine hydrolyzable polymer structures: one neat cross-linker network, one randomly cross-linked network of methyl methacrylate (MMA), and seven star-shaped polymers of MMA. Gel permeation chromatography (GPC) in tetrahydrofuran (THF) confirmed the narrow molecular weight distributions of the linear polymer precursors to the stars and demonstrated the increase in molecular weight upon the addition of cross-linker for the formation of star-shaped polymers. Characterization of the star polymers in THF using static light scattering and GPC showed that the molecular weights and the number of arms of each star polymer increased with an increase in the molar ratio of cross-linker to initiator and with a decrease in the molar ratio of monomer to initiator. The star polymers with DMOEM cores bore a smaller number of arms than those cross-linked with the non-hydrolyzable commercial cross-linker ethylene glycol dimethacrylate due to the bulkier structure of DMOEM. All DMOEM-containing polymer networks and star polymers were completely hydrolyzed within 48 h using hydrochloric acid in THF.

Synthesis and characterization of star polymers and cross-linked star polymer model networks containing a novel, silicon-based, hydrolyzable cross-linker

An acid-labile dimethacrylate cross-linker, dimethyldi(methacryloyloxy-l-ethoxy)silane (DMDMAES), was synthesized by the reaction of 2-hydroxyethyl methacrylate (HEMA) and dichlorodimethylsilane in the presence of triethylamine. Group transfer polymerization (GTP) was employed to use this cross-linker in the preparation of six hydrolyzable polymer structures: one neat cross-linker network, one randomly cross-linked network of methyl methacrylate (MMA), two star-shaped polymers of MMA, and two cross-linked star polymer model networks (CSPMNs) of MMA. A nonhydrolyzable CSPMN of MMA, based on a stable cross-linker, was also synthesized. Gel permeation chromatography (GPC) in tetrahydrofuran (THF) confirmed the narrow molecular weight distributions (MWDs) of the linear polymer precursors and demonstrated the increase in molecular weight (MW) upon each successive addition of cross-linker or monomer. Characterization by static light scattering (SLS) and GPC showed that star polymers with DMDMAES cores bear a relatively small number of arms, around 7. All star polymers and polymer networks were hydrolyzed using hydrochloric acid in THF. While the MWs of the products from the hydrolysis of the star polymers, the neat cross-linker network, and the randomly cross-linked network were as expected, those from the CSPMNs were of a much higher than expected MW, indicating extensive star-star coupling.

Establishing optimal quantitative-polymerase chain reaction assays for routine diagnosis and tracking of minimal residual disease in JAK2-V617F-associated myeloproliferative neoplasms:a joint European LeukemiaNet/MPN&MPNr-EuroNet (COST action BM0902) study

Reliable detection of JAK2-V617F is critical for accurate diagnosis of myeloproliferative neoplasms (MPNs); in addition, sensitive mutation-specific assays can be applied to monitor disease response. However, there has been no consistent approach to JAK2-V617F detection, with assays varying markedly in performance, affecting clinical utility. Therefore, we established a network of 12 laboratories from seven countries to systematically evaluate nine different DNA-based quantitative PCR (qPCR) assays, including those in widespread clinical use. Seven quality control rounds involving over 21,500 qPCR reactions were undertaken using centrally distributed cell line dilutions and plasmid controls. The two best-performing assays were tested on normal blood samples (n=100) to evaluate assay specificity, followed by analysis of serial samples from 28 patients transplanted for JAK2-V617F-positive disease. The most sensitive assay, which performed consistently across a range of qPCR platforms, predicted outcome following transplant, with the mutant allele detected a median of 22 weeks (range 6-85 weeks) before relapse. Four of seven patients achieved molecular remission following donor lymphocyte infusion, indicative of a graft vs MPN effect. This study has established a robust, reliable assay for sensitive JAK2-V617F detection, suitable for assessing response in clinical trials, predicting outcome and guiding management of patients undergoing allogeneic transplant.

Structural Capital of University Spin-Out Firms: The Moderating Role of University Incubators

University incubators (UI) are generally believed to be important in the successful commercialisation of university spin-outs (USO) with over half of all UK Universities having established an on-campus UI. In this chapter we examine the value of UIs in the spin-out process, focusing on the structural networks of USOs located in a UI as compared to USOs in a University with no access to a UI. Our primary research question is therefore: to what extent does the structural network of USOs with access to an on-campus UI differ from USOs without? The research therefore con-tributes to a growing critique of the effectiveness of UIs in commercialis-ing academic research and the recognition of positive direct and indirect externalities from participation in networks. Through network mapping of all USOs from two research intensive universities, we profile and ana-lyse the formal and informal network ties of USOs to various partners in-ternal and external to the host university. Through interviews we also consider how these networks enhance the resources and capabilities of USOs. Our findings highlight significant differences, with USOs located in a UI having more informal but fewer formal ties, both to other USOs as well as within the host University. In contrast, location in an incuba-tor was not found to affect the extent and nature of ties with external or-ganisations. Reasons for these differences are examined through inter-views with the USOs and point to various factors including the proactive brokering role of incubator and university staff, university bureaucracy, the hidden networks of executive board members across USOs, university equity investment policy and complementary technologies.

Towards optimal clinical and epidemiological registration of haematological malignancies: Guidelines for recording progressions, transformations and multiple diagnoses

Haematological malignancies (HM) represent over 6% of the total cancer incidence in Europe and affect all ages, ranging between 45% of all cancers in children and 7% in the elderly. Thirty per cent of childhood cancer deaths are due to HM, 8% in the elderly. Their registration presents specific challenges, mainly because HM may transform or progress in the course of the disease into other types of HM. In the context of cancer registration decisions have to be made about classifying subsequent notifications on the same patient as the same tumour (progression), a transformation or a new tumour registration. Allocation of incidence date and method of diagnosis must also be standardised. We developed European Network of Cancer Registries (ENCR) recommendations providing specific advice for cancer registries to use haematology and molecular laboratories as data sources, conserve the original date of incidence in case of change of diagnosis, make provision for recording both the original as well as transformed tumour and to apply precise rules for recording and counting multiple diagnoses. A reference table advising on codes which reflect a potential transformation or a new tumour is included. This work will help to improve comparability of data produced by population-based cancer registries, which are indispensable for aetiological research, health care planning and clinical research, an increasing important area with the application of targeted therapies.

Vitamin D and mortality: meta-analysis of individual participant data from a large consortium of cohort studies from Europe and the United States

Objective: To investigate the association between serum 25-hydroxyvitamin D concentrations (25(OH)D) and mortality in a large consortium of cohort studies paying particular attention to potential age, sex, season, and country differences.

Design: Meta-analysis of individual participant data of eight prospective cohort studies from Europe and the US.

Setting: General population.

Participants: 26 018 men and women aged 50-79 years

Main outcome measures: All-cause, cardiovascular, and cancer mortality.

Results: 25(OH)D concentrations varied strongly by season (higher in summer), country (higher in US and northern Europe) and sex (higher in men), but no consistent trend with age was observed. During follow-up, 6695 study participants died, among whom 2624 died of cardiovascular diseases and 2227 died of cancer. For each cohort and analysis, 25(OH)D quintiles were defined with cohort and subgroup specific cut-off values. Comparing bottom versus top quintiles resulted in a pooled risk ratio of 1.57 (95% CI 1.36 to 1.81) for all-cause mortality. Risk ratios for cardiovascular mortality were similar in magnitude to that for all-cause mortality in subjects both with and without a history of cardiovascular disease at baseline. With respect to cancer mortality, an association was only observed among subjects with a history of cancer (risk ratio, 1.70 (1.00 to 2.88)). Analyses using all quintiles suggest curvilinear, inverse, dose-response curves for the aforementioned relationships. No strong age, sex, season, or country specific differences were detected. Heterogeneity was low in most meta-analyses.

Conclusions: Despite levels of 25(OH)D strongly varying with country, sex, and season, the association between 25(OH)D level and all-cause and cause-specific mortality was remarkably consistent. Results from a long term randomised controlled trial addressing longevity are being awaited before vitamin D supplementation can be recommended in most individuals with low 25(OH)D levels.

'The End of the Irish Poor Law?: Welfare and Healthcare Reform in Revolutionary and Independent Ireland'

This book explores welfare provision in Ireland from the revolutionary period to the 1940s, This work is a significant addition to the growing historiography of twentieth-century Ireland which moves beyond political history. It demonstrates that concepts of respectability, deservingness, and social class where central dynamics in Irish society and welfare practices. This book provides the first major study of local welfare practices, policies, and attitudes towards poverty and the poor in this era.

This book’s exploration of the poor law during revolutionary and independent Ireland provides fresh and original insights into this critical juncture in Irish history. It charts the transformation of the former workhouse system into a network of local authority welfare and healthcare institutions including county homes, county and hospital hospitals, and mother and baby homes. This book provides historical context to current day debates and controversies relating to the institutionalisation of unwed mothers and child welfare policies.

This book undertakes two cases studies on county Kerry and Cork city; also, Irish experiences are placed against the backdrop of wider transnational trends.

This work has multiple audiences and will appeal to those interested in Irish social, culture, economic and political history. This book will also appeal to historians of welfare, the poor law, and the social history of medicine. It also informs modern-day social affairs.