Informatics-guided procurement of patient samples for biomarker discovery projects in cancer research

Modern cancer research for biomarker discovery program requires solving several tasks that are directly involved with patient sample procurement. One requirement is to construct a highly efficient workflow on the clinical side for the procurement to generate a consistent supply of high quality samples for research. This undertaking needs a network of interdepartmental collaborations and participations at various levels, including physical human interactions, information technology implementations and a bioinformatics tool that is highly effective and user-friendly to busy clinicians and researchers associated with the sample procurement. Collegial participation that is sequential but continual from one department to another demands dedicated bioinformatics software coordinating between the institutional clinic and the tissue repository facility. Participants in the process include admissions, consenting process, phlebotomy, surgery center and pathology. During this multiple step procedures, clinical data are collected for detailed analytical endpoints to supplement logistics of defining and validating the discovery of biomarkers.

The Use of Human Tissue

The use of human tissue raises ethical issues of great concern to health care professionals, biomedical researchers, ethics committees, tissue banks and policy makers because of the heightened importance given to informed consent and patient autonomy. The debate has been intensified by high profile scandals such as the “baby hearts” debacle and revelations about the retention of human brains in neuropathology laboratories worldwide. Respect for patient’s rights seems, however, to impede research and development of clinical knowledge in contemporary health care. The Common clinical endeavour argument and a Presumption for beneficial use argument suggest that the use of tissues for research and teaching in contemporary health care can respect patients and their values in multicultural communities where there are provisions for oversight and for opting not to contribute, both of which should respect the diverse views of different ethnic or cultural groups.

Gridcast—a next generation broadcast infrastructure?

Gridcast is an R&D project investigating grid ideas and technologies in the broadcasting technical infrastructure. In this paper I discuss the business and technical issues in building infrastructures to support broadcasters and outline the structure of the Gridcast grid-based service oriented architecture for broadcasting playout support.

Ecological and population genetics research imperatives for transgenic trees

Applied research that supplies requisite, albeit incomplete, scientific knowledge is necessary if we are to address the legal, regulatory, and social/ethical issues regarding the use of transgenic trees. The technology for creating these trees has gotten far ahead of research on the ecological and population genetics impacts that may emerge. In this paper, we propose a comprehensive, interdisciplinary scientific approach that combines experimental results with model projections. We believe that much of this work must be completed before social issues can be clarified and resolved. Broad-based failure by those in the forestry-minded scientific community to carry out this interdisciplinary research could lead either to the establishment of transgenic trees with unintended consequences, or to an inability to realize the numerous advantages that this technology may offer.

Individual variability of behavioural responses by Wandering Albatrosses (Diomedea exulans) to human disturbance

Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.

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Genomic Error-Correcting Codes in the Living World

This paper is intended to complement our previous works on the necessary existence of error-correcting codes endowing genomes with the ability of being regenerated, not merely copied. It sketchily recalls some fundamental definitions and results of information theory and error-correcting codes; provides an overview of our research; shows that the disjunction of replication and regeneration enlightens the divide between germinal and somatic cells; suggests that some phenomena referred to as epigenetic may possibly find an explanation within the framework of error-correcting codes; points out some difficulties, especially those related to sexual reproduction; criticizes the template-replication paradigm, and prompts geneticists to become familiar with information theory.

Syndromic Surveillance and Patients as Victims and Vectors

Syndromic surveillance uses new ways of gathering data to identify possible disease outbreaks. Because syndromic surveillance can be implemented to detect patterns before diseases are even identified, it poses novel problems for informed consent, patient privacy and confidentiality, and risks of stigmatization. This paper analyzes these ethical issues from the viewpoint of the patient as victim and vector. It concludes by pointing out that the new International Health Regulations fail to take full account of the ethical challenges raised by syndromic surveillance.

Microarray Applications in Microbial Ecology Research

Microarray technology has the unparalleled potential to simultaneously determine the dynamics and/or activities of most, if not all, of the microbial populations in complex environments such as soils and sediments. Researchers have developed several types of arrays that characterize the microbial populations in these samples based on their phylogenetic relatedness or functional genomic content. Several recent studies have used these microarrays to investigate ecological issues; however, most have only analyzed a limited number of samples with relatively few experiments utilizing the full high-throughput potential of microarray analysis. This is due in part to the unique analytical challenges that these samples present with regard to sensitivity, specificity, quantitation, and data analysis. This review discusses specific applications of microarrays to microbial ecology research along with some of the latest studies addressing the difficulties encountered during analysis of complex microbial communities within environmental samples. With continued development, microarray technology may ultimately achieve its potential for comprehensive, high-throughput characterization of microbial populations in near real time.

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Sexual selection and mate choice in evolutionary psychology

The importance of mate choice and sexual selection has been emphasized by the majority of evolutionary psychologists. This paper assesses three cases of work on mate choice and sexual selection in evolutionary psychology: David Buss on cross-cultural human mate preferences, Randy Thornhill and Steve Gangestad on the link between mate preferences and fluctuating asymmetry, and Geoffrey Miller on the role of Fisher’s runaway process in human evolution. A mixture of conceptual and empirical problems in each case highlights the general weakness of work in evolutionary psychology on these issues.

A simple and fast method for cell recovery and DNA content analysis from various mouse tissues by flow cytometry

Cell division in tissues can be investigated in various ways. We present here a method for improving cell recovery and cell cycle analysis for a wide range of mouse tissues. This strategy combines a cell isolation procedure for various mouse tissues based on intracardiac perfusion and subsequent treatment followed by flow cytometry. This easy and reproducible method allows a rapid analysis of nuclear DNA content, providing an estimate of the cell number at different phases of the cell cycle. This combined procedure could also be used for the isolation of specific cell subpopulations from different mouse tissues by fluorescence activated cell sorting.

Leitlinien zur molekulargenetischen Diagnostik: Fragiles-X und Fragiles-X assoziiertes Tremor/Ataxie Syndrom

Ohne Zusammenfassung

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Grid user requirements—2004: a perspective from the trenches

Pervasive Grid adoption is predicated on the availability of widely deployed usable software and a user community willing to use it. Currently, widespread adoption of Grids, even within technically sophisticated communities, is limited, and determining and eliminating these barriers to adoption are essential in order for Grids to becoming widely capitalized. Through a series of face-to-face interviews conducted during the summer of 2004, we have identified issues relating to job submission, file transfer, usability, and systems management that must be resolved in order to improve the usability of Grid infrastructures. The background to these issues and some possible solutions are described in this paper.

Capacity-Building for Natural Resource Management: Lessons from the Health Sector

This paper examines capacity-building measures used by the health sector relevant to natural resource management (NRM) using the delivery of two programs in Australia through its recently formalized 56 community-based regional NRM Boards as a reference point. The delivery of NRM outcomes through devolved governance arrangements has been hampered by inadequate capacity in other countries (e.g., New Zealand, Canada). The inherent complexities of NRM, coupled with professional “comfort zones,” often limit actors from looking to other sectors confronting similar issues. This paper summarizes findings from ∼70 sources in health reviewing nine major capacity-building measures. The outcomes of research evaluating the relative benefits and disbenefits of applying these measures are discussed. The paper identifies several opportunities to trial some of these measures in NRM.

Ethics in Indigenous Research – Connecting with Community

The challenge for those responsible for funding, brokering and assessing the merit of proposed Indigenous research is to identify and then work co-operatively with appropriate representatives of Indigenous interests in order to increase the flow of benefits from research to Indigenous peoples. Experience in Australia has shown that this is not a straightforward process. In this paper we indicate some reasons why it is important for the research community to broker research with representative Indigenous organisations and to involve Indigenous peoples in the ethical assessment and conduct of research. We then identify some barriers to the achievement of these objectives and outline recently developed interventions from the field of health research that aim to promote a more effective working relationship between Indigenous peoples and members of the research community.

Multiple realization in comparative perspective

Arguments for multiple realization depend on the idea that the same kind of function is realized by different kinds of structures. It is important to such arguments that we know the kinds used in the arguments have been individuated properly. In the philosophical literature, though, claims about how to individuate kinds are frequently decided on intuitive grounds. This paper criticizes this way of approaching kinds by considering how practicing researchers think about the matter. I will consider several examples in which the practice of researchers on comparative vision conflicts with the standard account of these issues.

Hierarchical analysis of piecewise affine models of gene regulatory networks

A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions. In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly connected components decomposition, is not new. However, its adaptation to the non-smooth PWA differential equations turns out to be quite relevant because of the strong discrete structure underlying these equations. Its biological relevance is shown on a 7-dimensional PWA system modeling the gene network responsible for the carbon starvation response in Escherichia coli.

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