Highly sensitive determination of the methylated p16 gene in cancer patients by microchip electrophoresis

The p16 tumor suppressor gene is inactivated by promoter region hypermethylation in many types of tumor. Recent studies showed that aberrant methylation of the p16 gene is an early event in many tumors, especially in lung cancer, and may constitute a new biomarker for early detection and monitoring of prevention trials. We detected tumor-associated aberrant hypermethylation of the p16 gene in plasma and tissue DNA from 153 specimens using a modified semi-nested methylation-specific PCR (MSP) combining plastic microchip electrophoresis or slab gel electrophoresis, respectively. Specimens were from 79 lung cancer patients, 15 abdominal tumor patients, 30 positive controls and 30 negative controls. The results showed that the positive rate obtained by microchip electrophoresis was more than 26.6% higher and the same speciticity was kept when compared with slab gel electrophoresis. The microchip electrophoresis can rapidly and accurately analyze the PCR products of methylated DNA and obviously improve the positive rate of diagnosis of cancer patients when compared with gel electrophoresis. This method with the high assay sensitivity might be used for detection of methylation of p16 gene and even to facilitate early diagnosis of cancer patients. (C) 2004 Elsevier B.V. All rights reserved.

Planning the deployment of fault-tolerant wireless sensor networks

Since Wireless Sensor Networks (WSNs) are subject to failures, fault-tolerance becomes an important requirement for many WSN applications. Fault-tolerance can be enabled in different areas of WSN design and operation, including the Medium Access Control (MAC) layer and the initial topology design. To be robust to failures, a MAC protocol must be able to adapt to traffic fluctuations and topology dynamics. We design ER-MAC that can switch from energy-efficient operation in normal monitoring to reliable and fast delivery for emergency monitoring, and vice versa. It also can prioritise high priority packets and guarantee fair packet deliveries from all sensor nodes. Topology design supports fault-tolerance by ensuring that there are alternative acceptable routes to data sinks when failures occur. We provide solutions for four topology planning problems: Additional Relay Placement (ARP), Additional Backup Placement (ABP), Multiple Sink Placement (MSP), and Multiple Sink and Relay Placement (MSRP). Our solutions use a local search technique based on Greedy Randomized Adaptive Search Procedures (GRASP). GRASP-ARP deploys relays for (k,l)-sink-connectivity, where each sensor node must have k vertex-disjoint paths of length ≤ l. To count how many disjoint paths a node has, we propose Counting-Paths. GRASP-ABP deploys fewer relays than GRASP-ARP by focusing only on the most important nodes – those whose failure has the worst effect. To identify such nodes, we define Length-constrained Connectivity and Rerouting Centrality (l-CRC). Greedy-MSP and GRASP-MSP place minimal cost sinks to ensure that each sensor node in the network is double-covered, i.e. has two length-bounded paths to two sinks. Greedy-MSRP and GRASP-MSRP deploy sinks and relays with minimal cost to make the network double-covered and non-critical, i.e. all sensor nodes must have length-bounded alternative paths to sinks when an arbitrary sensor node fails. We then evaluate the fault-tolerance of each topology in data gathering simulations using ER-MAC.

Exploring processes of indeterminate determinism in music composition, programming and improvisation

This portfolio consists of 15 original musical works. Taking the form of electronic and acousmatic music, multimedia, and scores, these chamber works serve as a result of experimentation and improvisation with individually built computer interfaces. The accompanying commentary provides discourse on the conceptual practice of these interfaces becoming a compositional entity that present a multi-interpretative opportunity to explore, engage, and personalise. Following this, the commentary examines the path of creative decisions and musical choices that formed both these interfaces and the resulting musical and visual works. This portfolio is accompanied by interfaces used, transcoded interfacing behavioural information, and documented improvisational findings.

El tráfico de la maquinaria en diferentes sistemas de labranza y su incidencia sobre la compactación del suelo y el rendimiento del maíz (Zea mays L.) en el partido de Luján

El establecimiento del cultivo depende fundamentalmente de los métodos utilizados para la preparación del suelo y la siembra. Nuestro principal objetivo fue evaluar la compactación del suelo y los efectos de los residuos de la cosecha del maíz (Zea Mays L.) sobre la emergencia de las plántulas y los rendimientos en tres diferentes métodos de labranza: siembra directa (SD), arado de cincel (CN) y arado de reja y vertedera (AV). El estudio se realizó al este de la región pampeana entre Octubre de 2004 y Marzo de 2007. El suelo del sitio de estudio es un Argiudol típico. Nuestras hipótesis de trabajo fueron: a) que los rendimientos de maíz se ven afectados por los métodos de labranza utilizados para la preparación del suelo, y b) que el tráfico, en los tres métodos de labranza, causa compactación subsuperficial del suelo. Las variables medidas fueron: (1) Índice de cono (IC) ) entre 0 y 450 mm, (2) la materia seca de la raíz por planta (MSR), (3) materia seca por planta (MSP), (4) la emergencia de plántulas (EP), y (5) los rendimientos del maíz (RM). Los resultados mostraron que en SD, el nivel de compactación del suelo causo menores rendimientos (disminución entre el 10,7 y el 15,2 por ciento) en comparación con CN y AV. La EP fue más lenta en CN y de AV en comparación con SD, pero resultados similares se obtuvieron 18 días después de la siembra. Los valores más altos MSR se observaron en CN y AV (42,3 y 46,1 g planta-1, respectivamente) en comparación con el SD (37,1 g planta-1). El estudio arrojó las siguientes conclusiones. El RM está directamente relacionado con la MSR por planta, que se vio afectada por la compactación del suelo. El horizonte Ap del suelo tiene que ser labrado para mejorar el RM. A pesar del mayor número de pasadas de equipos en el CN y el AV, todos los sistemas labranza causaron compactación del subsuelo. La EP no se vio afectada por el rastrojo del cultivo.

‘A system that works for the sea’? Exploring Stakeholder Engagement in Marine Spatial Planning

This paper aims to contribute to the current debate on Marine Spatial Planning (MSP) by exploring the issue of stakeholder engagement. MSP is an emergent policy field that is subject to an increasing body of research, yet the role, scope and nature of participatory engagement within the process remains a neglected topic. This paper briefly reviews the nature of the ‘marine problem’, to which MSP is seen to be the response and describes the emergence of MSP policy in the UK with specific emphasis on participatory aspects. Drawing on the experience of terrestrial planning it discusses the potential benefits of stakeholder engagement in MSP and highlights some of the key issues that need to be taken into account when shaping stakeholder input into the process. It then goes on to describe the findings from a series of interviews with key stakeholders in the Irish Sea Region, which suggest that we need to develop a more critical and deeper understanding of how various interests frame the ‘marine problem’, and how they see their role in shaping the form of the MSP process. This highlights the importance of encouraging stakeholder involvement in MSP, the need to develop a shared vision of a ‘sea interest’. Priorities are then set for research to support this important policy agenda.

LyonPotpourri 3.0

A set of audio signal processing software for Max/MSP and Pure Data.

RUNX3 Inactivation in Colorectal Polyps Arising Through Different Pathways of Colonic Carcinogenesis

OBJECTIVES: We hypothesized that RUNX3 inactivation by promoter hypermethylation in colorectal polyps is an early molecular event in colorectal carcinogenesis.
METHODS: RUNX3 protein expression was analyzed immunohistochemically in 50 sporadic colorectal polyps comprising 19 hyperplastic polyps (HPs), 14 traditional serrated adenomas (TSAs), and 17 sporadic traditional adenomas (sTAs) as well as in 19 familial adenomatous polyposis (FAP) samples from 10 patients showing aberrant crypt foci (ACF) (n=91), small adenomas (SmAds) (n=40), and large adenomas (LAds) (n=13). In addition, we assessed the frequency of promoter hypermethylation of RUNX3 by methylation-specific PCR (MSP) in all the 50 sporadic polyps as well as 38 microdissected FAP polyps comprising ACF, SmAds, and LAds obtained from 7 FAP samples. A total of 12 normal colon samples were also included for RUNX3 MSP analysis.
RESULTS: Compared to normal colon (2 of 12, 16%) and sTAs (3 of 17, 18%), HPs (15 of 19, 79%) and TSAs (8 of 14, 57%) displayed significant inactivation of RUNX3 (P<0.05). In FAP, RUNX3 inactivation was more frequently seen in ACF (78 of 91, 86%), SmAds (25 of 40, 62%), and LAds (6 of 13, 46%) compared to normal mucosa (0 of 19, 0%) in the same samples (all P<0.05). Promoter hypermethylation of RUNX3 was significantly higher in colorectal polyps (64 of 87, 74%) compared to normal colon (2 of 12, 16%) (P=0.001). Serrated polyps such as HPs (17 of 19, 89%) and TSAs (12 of 14, 86%) were significantly more methylated than sTAs (7 of 17, 44%) (P=0.004). RUNX3 hypermethylation was observed in 28 of the total 38 (74%) FAP polyps. Overall, RUNX3 promoter methylation correlated with inactivation of RUNX3 expression in sporadic (27 of 36, 75%) (P=0.022) and FAP (21 of 28, 75%) (P=0.021) polyps.
CONCLUSIONS: Our data suggest that RUNX3 inactivation due to promoter hypermethylation in colorectal polyps represents an early event in colorectal cancer (CRC) progression. In addition, epigenetic RUNX3 inactivation is a frequent event in the serrated colonic polyps as well as in the ACF of FAP polyps.

From the Land to Sea and Back Again? Using Terrestrial Planning to Understand the Process of Marine Spatial Planning

Over the last 5–10 years, marine spatial planning (MSP) has emerged as a new management regime for national and international waters and has already attracted a substantial body of multi-disciplinary research on its goals and policy processes. This paper argues that this literature has generally lacked deeper reflexive engagement with the emerging system of governance for our seas that has meant that many of MSP’s core concepts, assumptions and institutional arrangements have not been subject rigorous intellectual debate. In an attempt to initiate such an approach, this article explores the relationship between MSP and its land-based cousin, terrestrial spatial planning (TSP). While it is recognized that there are inherent limitations to a comparison of these two systems, it is argued that the tradition of social science debate over the purpose and processes of TSP can be used as a useful stimulus for a more rigorous reflection of such issues as they relate to MSP. The article therefore explores some of the parallels between MSP and TSP and then discusses some of the key intellectual traditions that have shaped TSP and the implications these may have for future marine planning practice. The article concludes with a number of potentially useful new avenues that may form the basis of a critical research agenda for MSP.

Obfuscation: The Hidden Malware

A cyberwar exists between malware writers and antimalware researchers. At this war's heart rages a weapons race that originated in the 80s with the first computer virus. Obfuscation is one of the latest strategies to camouflage the telltale signs of malware, undermine antimalware software, and thwart malware analysis. Malware writers use packers, polymorphic techniques, and metamorphic techniques to evade intrusion detection systems. The need exists for new antimalware approaches that focus on what malware is doing rather than how it's doing it.

Deriving lessons relating to marine spatial planning from Canada's Eastern Scotian Shelf Integrated Management Initiative

Stakeholder participation is viewed as a key element of ecosystem-based marine spatial planning (MSP). There is much debate over the effectiveness of stakeholder participation in ecosystem-based management (EBM) in general and over the form it should take. Particular challenges relating to participation in the marine environment are highlighted. A study of the Eastern Scotian Shelf Integrated Management initiative, which uses a collaborative planning model to implement EBM, is presented in order to explore these issues further. Criteria derived from a review of collaborative planning literature are employed to evaluate the effectiveness of this model, which is found to be a useful consensus-building tool. Although a strategic-level plan has been adopted, the initiative has encountered difficulties transitioning from plan development to plan implementation. These are attributable in large measure to deficiencies in the design of the collaborative model. Useful lessons relating mainly to stakeholder engagement, the role of the lead agency, and implementation strategies are advanced for those engaging in MSP processes.

Preparing the ground for marine spatial planning in Ireland

Marine spatial planning (MSP) is advocated as a means of managing human uses of the sea in a manner that is consistent with the maintenance of the ecological goods and services of the marine environment. The adoption of a system of MSP is seen as urgent in the face of ever-increasing demands on marine resources. This is particularly so in Ireland with its extensive seas, belatedly being recognised as a significant development resource. MSP is promoted by the European Commission (EC) in a recent Green Paper to which Member States of the Union, including Ireland, generally have responded positively. Arising from this consultative process, the EC has published the 'Blue Book' that commits support for MSP. It has also issued guidelines for an integrated approach to maritime policy. The recently adopted EU Marine Strategy Framework Directive strengthens the case for implementing MSP as it requires each Member State to develop a strategy for its marine resources. There is evidence that a diverse range of stakeholders at national and local levels in Ireland are positively disposed toward MSP but no practical manifestation of the concept is in place, though some preparatory work is underway to facilitate its likely implementation into the future. © 2010 WIT Press.

Stakeholder Participation in Marine Spatial Planning:Lessons from the Channel Islands National Marine Sanctuary

Stakeholder participation is advanced as a key element of marine spatial planning (MSP) by the U.S. Interagency Ocean Policy Task Force. It provides little guidance, however, regarding stakeholder participation. We argue that much can be learned from existing ecosystem-based marine management initiatives. The Channel Islands National Marine Sanctuary, which utilizes an advisory council to facilitate stakeholder participation, is evaluated in this article with a view to identifying key lessons for new MSP initiatives. A set of criteria, derived from collaborative planning theory, is employed to evaluate the effectiveness of this approach. The advisory council meets some criteria for effective stakeholder participation but is found to be lacking in key elements, including shared purpose and interdependency. Benefits associated with stakeholder participation are constrained accordingly. Deficiencies in the design of the council and its decision-making procedures, requiring attention in order to facilitate more effective stakeholder participation in new MSP initiatives, are highlighted. © 2012 Copyright Taylor and Francis Group, LLC.

Marine spatial planning from the perspective of a small seaside community in Ireland

Marine spatial planning (MSP) is advocated as a means of managing human uses of the sea in a manner that is consistent with the maintenance of the ecological goods and services of the marine environment. Support for the process is evident at international and national levels but the degree to which it is acceptable to local level stakeholders is not clear. An Daingean (formely Dingle) is a small sea-oriented town situated on the southwest coast of Ireland in which marine-based tourism and other relatively new uses of the sea are pursued along side traditional fishing activities. Stakeholders in An Daingean are found to be positively disposed to a local process of MSP that incorporates meaningful local involvement.