Reflections on Mira : interactive evaluation in information retrieval

Evaluation in information retrieval (IR) has focussed largely on noninteractive evaluation of text retrieval systems. This is increasingly at odds with how people use modern IR systems: in highly interactive settings to access linked, multimedia information. Furthermore, this approach ignores potential improvements through better interface design. In 1996 the Commission of the European Union Information Technologies Programme, funded a three year working group, Mira, to discuss and advance research in the area of evaluation frameworks for interactive and multimedia IR applications. Led by Keith van Rijsbergen, Steve Draper and myself from Glasgow University, this working group brought together many of the leading researchers in the evaluation domain from both the IR and human computer interaction (HCI) communities. This paper presents my personal view of the main lines of discussion that took place throughout Mira: importing and adapting evaluation techniques from HCI, evaluating at different levels as appropriate, evaluating against different types of relevance and the new challenges that drive the need for rethinking the old evaluation approaches. The paper concludes that we need to consider more varied forms of evaluation to complement engine evaluation

Evidence-based medicine and progress in the medical sciences

The question what scientific progress means for a particular domain such as medicine seems importantly different from the question what scientific progress is in general. While the latter question received ample treatment in the philosophical literature, the former question is hardly discussed. I argue that it is nonetheless important to think about this question in view of the methodological choices we make. I raise specific questions that should be tackled regarding scientific progress in the medical sciences and demonstrate their importance by means of an analysis of what evidence-based medicine (EBM) has, and has not, to offer in terms of progress. I show how critically thinking about EBM from the point of view of progress can help us in putting EBM and its favoured methodologies in the right perspective. My conclusion will be that blindly favouring certain methods because of their immediately tangible short-term benefits implies that we parry the important question of how best to advance progress in the long run. This leads us to losing sight of our general goals in doing research in the medical sciences

Aquatic community response to volcanic eruptions on the Ecuadorian Andean flank: evidence from the palaeoecological record

Aquatic ecosystems in the tropical Andes are under increasing pressure from human modification of the landscape (deforestation and dams) and climatic change (increase of extreme events and 1.5 °C on average temperatures are projected for AD 2100). However, the resilience of these ecosystems to perturbations is poorly understood. Here we use a multi-proxy palaeoecological approach to assess the response of aquatic ecosystems to a major mechanism for natural disturbance, volcanic ash deposition. Specifically, we present data from two Neotropical lakes located on the eastern Andean flank of Ecuador. Laguna Pindo (1°27.132′S–78°04.847′W) is a tectonically formed closed basin surrounded by a dense mid-elevation forest, whereas Laguna Baños (0°19.328′S–78°09.175′W) is a glacially formed lake with an inflow and outflow in high Andean Páramo grasslands. In each lake we examined the dynamics of chironomids and other aquatic and semi-aquatic organisms to explore the effect of thick (> 5 cm) volcanic deposits on the aquatic communities in these two systems with different catchment features. In both lakes past volcanic ash deposition was evident from four large tephras dated to c.850 cal year BP (Pindo), and 4600, 3600 and 1500 cal year BP (Baños). Examination of the chironomid and aquatic assemblages before and after the ash depositions revealed no shift in composition at Pindo, but a major change at Baños occurred after the last event around 1500 cal year BP. Chironomids at Baños changed from an assemblage dominated by Pseudochironomus and Polypedilum nubifer-type to Cricotopus/Paratrichocladius type-II, and such a dominance lasted for approximately 380 years. We suggest that, despite potential changes in the water chemistry, the major effect on the chironomid community resulted from the thickness of the tephra being deposited, which acted to shallow the water body beyond a depth threshold. Changes in the aquatic flora and fauna at the base of the trophic chain can promote cascade effects that may deteriorate the ecosystem, especially when already influenced by human activities, such as deforestation and dams, which is frequent in the high Andes

Development and evaluation of an Individualised Outcome Measure (IOM) for randomised controlled trials in mental health

Predefined, researcher-selected outcomes are routinely used as the clinical end-point in randomised controlled trials (RCTs); however, individualised approaches may be an effective way to assess outcome in mental health research. The present study describes the development and evaluation of the Individualised Outcome Measure (IOM), which is a patient-specific outcome measure to be used for RCTs of complex interventions. IOM was developed using a narrative review, expert consultation and piloting with mental health service users (n=20). The final version of IOM comprises two components: Goal Attainment (GA) and Personalised Primary Outcome (PPO). For GA, patients identify one relevant goal at baseline and rate its attainment at follow-up. For PPO, patients choose an outcome domain related to their goal from a predefined list at baseline, and complete a standardised questionnaire assessing the chosen outcome domain at baseline and follow-up. A feasibility study indicated that IOM had adequate completion (89%) and acceptability (96%) rates in a clinical sample (n=84). IOM was then evaluated in an RCT (ISRCTN02507940). GA and PPO components were associated with each other and with the trial primary outcome. The use of the PPO component of IOM as the primary outcome could be considered in future RCTs

Green fluorescent protein-based expression screening of membrane proteins in Escherichia coli.

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and the inherent instability of many membrane proteins once solubilized in detergents. A protocol is described that combines ligation independent cloning of membrane proteins as GFP fusions with expression in Escherichia coli detected by GFP fluorescence. This enables the construction and expression screening of multiple membrane protein/variants to identify candidates suitable for further investment of time and effort. The GFP reporter is used in a primary screen of expression by visualizing GFP fluorescence following SDS polyacrylamide gel electrophoresis (SDS-PAGE). Membrane proteins that show both a high expression level with minimum degradation as indicated by the absence of free GFP, are selected for a secondary screen. These constructs are scaled and a total membrane fraction prepared and solubilized in four different detergents. Following ultracentrifugation to remove detergent-insoluble material, lysates are analyzed by fluorescence detection size exclusion chromatography (FSEC). Monitoring the size exclusion profile by GFP fluorescence provides information about the mono-dispersity and integrity of the membrane proteins in different detergents. Protein: detergent combinations that elute with a symmetrical peak with little or no free GFP and minimum aggregation are candidates for subsequent purification. Using the above methodology, the heterologous expression in E. coli of SED (shape, elongation, division, and sporulation) proteins from 47 different species of bacteria was analyzed. These proteins typically have ten transmembrane domains and are essential for cell division. The results show that the production of the SEDs orthologues in E. coli was highly variable with respect to the expression levels and integrity of the GFP fusion proteins. The experiment identified a subset for further investigation

Polymer transport in random flow

The dynamics of polymers in a random smooth flow is investigated in the framework of the Hookean dumbbell model. The analytical expression of the time-dependent probability density function of polymer elongation is derived explicitly for a Gaussian, rapidly changing flow. When polymers are in the coiled state the pdf reaches a stationary state characterized by power-law tails both for small and large arguments compared to the equilibrium length. The characteristic relaxation time is computed as a function of the Weissenberg number. In the stretched state the pdf is unstationary and exhibits multiscaling. Numerical simulations for the two-dimensional Navier-Stokes flow confirm the relevance of theoretical results obtained for the delta-correlated model.Comment: 28 pages, 6 figure

Dynamics of stick-slip in peeling of an adhesive tape

We investigate the dynamics of peeling of an adhesive tape subjected to a constant pull speed. We derive the equations of motion for the angular speed of the roller tape, the peel angle and the pull force used in earlier investigations using a Lagrangian. Due to the constraint between the pull force, peel angle and the peel force, it falls into the category of differential-algebraic equations requiring an appropriate algorithm for its numerical solution. Using such a scheme, we show that stick-slip jumps emerge in a purely dynamical manner. Our detailed numerical study shows that these set of equations exhibit rich dynamics hitherto not reported. In particular, our analysis shows that inertia has considerable influence on the nature of the dynamics. Following studies in the Portevin-Le Chatelier effect, we suggest a phenomenological peel force function which includes the influence of the pull speed. This reproduces the decreasing nature of the rupture force with the pull speed observed in experiments. This rich dynamics is made transparent by using a set of approximations valid in different regimes of the parameter space. The approximate solutions capture major features of the exact numerical solutions and also produce reasonably accurate values for the various quantities of interest.Comment: 12 pages, 9 figures. Minor modifications as suggested by refere

Propagation of ultrahigh energy nuclei in clusters of galaxies: resulting composition and secondary emissions

We study the survival of ultrahigh energy nuclei injected in clusters of galaxies, as well as their secondary neutrino and photon emissions, using a complete numerical propagation method and a realistic modeling of the magnetic, baryonic and photonic backgrounds. It is found that the survival of heavy nuclei highly depends on the injection position and on the profile of the magnetic field. Taking into account the limited lifetime of the central source could also lead in some cases to the detection of a cosmic ray afterglow, temporally decorrelated from neutrino and gamma ray emissions. We calculate that the diffusive neutrino flux around 1 PeV coming from clusters of galaxies may have a chance to be detected by current instruments. The observation of single sources in neutrinos and in gamma rays produced by ultrahigh energy cosmic rays will be more difficult. Signals coming from lower energy cosmic rays (E < 1 PeV), if they exist, might however be detected by Fermi, for reasonable sets of parameters.Comment: 19 pages, 15 figures, version to appear in ApJ (minor changes

The Lx-T and Lx-sigma Relationships for Galaxy Clusters Revisited

The relationships between the X-ray determined bolometric luminosity Lx, the temperature T of the intracluster gas, and the optical measured velocity dispersion sigma of the cluster galaxies are updated for galaxy clusters using the largest sample of 256 clusters drawn from literature. The newly established relationships, based on the doubly weighted orthogonal distance regression (ODR) method, are justified by both their self-consistency and co-consistency, which can then be used to test the theoretical models of cluster formation and evolution. The observationally determined Lx-T and Lx-sigma relationships, $L_x\propto T^{2.72\pm0.05}\propto \sigma^{5.24\pm0.29}$, are marginally consistent with those predicted in the scenario that both intracluster gas and galaxies are in isothermal and hydrostatic equilibrium with the underlying gravitational potential of clusters. A comparison between these observed and predicted Lx-T relationships also suggests that the mean cluster baryon fraction fb remains approximately constant among different clusters, $f_b\approx0.17$, which gives rise to a low-mass density universe of $\Omega_m\approx0.3$.Comment: 34 pages, 7 figures, 2 tables, accepted for publication in Ap