Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential

In this article, we focus on the analysis of competitive gene set methods for detecting the statistical significance of pathways from gene expression data. Our main result is to demonstrate that some of the most frequently used gene set methods, GSEA, GSEArot and GAGE, are severely influenced by the filtering of the data in a way that such an analysis is no longer reconcilable with the principles of statistical inference, rendering the obtained results in the worst case inexpressive. A possible consequence of this is that these methods can increase their power by the addition of unrelated data and noise. Our results are obtained within a bootstrapping framework that allows a rigorous assessment of the robustness of results and enables power estimates. Our results indicate that when using competitive gene set methods, it is imperative to apply a stringent gene filtering criterion. However, even when genes are filtered appropriately, for gene expression data from chips that do not provide a genome-scale coverage of the expression values of all mRNAs, this is not enough for GSEA, GSEArot and GAGE to ensure the statistical soundness of the applied procedure. For this reason, for biomedical and clinical studies, we strongly advice not to use GSEA, GSEArot and GAGE for such data sets.

Development of a technique to measure the residual strength of woodworm infested timber

This paper presents a study of the residual strength of Pinus sylvestris, which has been subject to attack by the furniture beetle (Anobium punctatum). It is relatively easy to stop the infestation, but difficult to assess the structural soundness of the remaining timber. Removal and replacement of affected structural elements is usually difficult and expensive, particularly in buildings of historic interest. Current on-site assessment procedures are limited. The main object of the study was to develop an on-site test of timber quality: a test which can be carried out on the surface and also at varying depths into the timber. It is based on a probe pull-out technique using a portable load-measuring device. Pull-out force values have been correlated with both strength and energy absorbed as measured by compression testing on laboratory samples of both sound and infested timber. These two relationships are significant and could be used to assess whether remedial work is needed. In addition, work on the use of artificial borings to simulate the natural worming of timber is presented and the findings discussed.

Possession Taken by Theft and the Original Acquisition of Personal Property Rights

This paper queries the soundness of the view that wrongful possession (eg a thief’s possession of goods he has stolen) should be protected by the standard actions for interference with goods. It uses close historical analysis of the development of the relevant concepts through the cases to argue that this is not a proposition that is compelled on the authorities, nor one demanded as a matter of principle. It then abstracts to consider the implications of this argument at a theoretical level, exposing great need for development in the common law’s basic principles of possessory protection. It argues innovatively that the objects of the law might be better served by the creation of a more limited form of possessory protection, achieved through the possessor’s acquisition of a personal right, and correlatively that the values that underpin and justify our basic rules of possessory protection entail a more nuanced response to matters of property acquisition.

D3.1 Benefits Analysis of the Initial Operational Cruiser-Feeder Concept

The REsearch on a CRuiser Enabled Air Transport Environment (RECREATE) project is considers the introduction and airworthiness of cruiser-feeder operations for civil aircraft. Cruiser-feeder operations are investigated as a promising pioneering idea for the air transport of the future. The soundness of the concept of cruiser-feeder operations for civil aircraft can be understood, taking air-to-air refueling operations as an example. For this example, a comprehensive estimate of the benefits can be made, which shows a fuel burn reduction potential and a CO2 emission reduction of 31% for a typical 6000 nautical miles flight with a payload of 250 passengers. This reduction potential is known to be large by any standard. The top level objective of the RECREATE project is to demonstrate on a preliminary design level that cruiser-feeder operations (as a concept to reduce fuel burn and CO2 emission levels) can be shown to comply with the airworthiness requirements for civil aircraft. The underlying Scientific and Technological (S&T) objectives are to determine and study airworthy operational concepts for cruiser-feeder operations, and to derive and quantify benefits in terms of CO2 emission reduction but also other benefits.

Work Package (WP) 3 has the objective to substantiate the assumed benefits of the cruiser/feeder operations through refined analysis and simulation. In this report, initial benefits evaluation of the initial RECREATE cruiser/feeder concepts is presented. The benefits analysis is conducted in delta mode, i.e. comparison is made with a baseline system. Since comparing different aircraft and air transport systems is never a trivial task, appropriate measures and metrics are defined and selected first. Non-dimensional parameters are defined and values for the baseline system derived.

The impact of cruiser/feeder operations such as air-to-air refueling are studied with respect to fuel-burn (or carbon-dioxide), noise and congestion. For this purpose, traffic simulations have been conducted.
Cruiser/feeder operations will have an impact on dispatch reliability as well. An initial assessment of the effect on dispatch reliability has been made and is reported.

Finally, a considerable effort has been made to create the infrastructure for economic delta analysis of the cruiser/feeder concept of operation. First results of the cost analysis have been obtained.

Assessing the needs of informal caregivers to cancer survivors: a review of the instruments

Objective: Cancer may impact negatively on an informal caregiver's health long after treatment has ended. This review identifies the self-report measures currently in use to measure caregivers need for support and determines their scientific soundness and clinical utility.

Method: A systematic electronic database search of Medline, CINAHL, PsychINFO, BNI ProQuest was conducted. The psychometric properties and clinical utility of needs assessment tools for caregivers of cancer survivors (excluding advanced disease) were extracted and summarised.

Results: Seven cancer survivor caregiver needs assessment tools were identified. Data on instrument development was well reported, although variability was noted in their structure and content. The majority demonstrated some degree of reliability and validity; only two were evaluated for test–retest reliability (CaSPUN and SPUNS) with only the SPUNS showing a high degree of reliability over time. The Health Care Needs Survey (HCNS), Needs Assessment of Family Caregivers-Cancer (NAFC-C) and Cancer Caregiving Tasks Consequences and Needs Questionnaire (CaTCoN) have been validated at various stages of the cancer continuum. Minimal data was available on responsiveness.

Conclusion: All assessment tools identified require further psychometric analysis. For research purposes, the use of the SPUNS (with its acceptable test–retest reliability) appears most appropriate; although its length may be of concern for clinical use; therefore, the shorter SCNS-P&C is likely to be more suitable for use clinically. At present, the NAFC-C demonstrates a great potential in both the research and clinical environments; however, it requires further psychometric testing before it can be fully recommended. Further analysis is necessary on ideal response formats and the meaning of a total needs score.