Statistical modelling of summary values leads to accurate Approximate Bayesian Computations

Approximate Bayesian Computation (ABC) methods rely on asymptotic arguments, implying that parameter inference can be systematically biased even when sufficient statistics are available. We propose to construct the ABC accept/reject step from decision theoretic arguments on a suitable auxiliary space. This framework, referred to as ABC*, fully specifies which test statistics to use, how to combine them, how to set the tolerances and how long to simulate in order to obtain accuracy properties on the auxiliary space. Akin to maximum-likelihood indirect inference, regularity conditions establish when the ABC* approximation to the posterior density is accurate on the original parameter space in terms of the Kullback-Leibler divergence and the maximum a posteriori point estimate. Fundamentally, escaping asymptotic arguments requires knowledge of the distribution of test statistics, which we obtain through modelling the distribution of summary values, data points on a summary level. Synthetic examples and an application to time series data of influenza A (H3N2) infections in the Netherlands illustrate ABC* in action.Comment: Videos can be played with Acrobat Reader. Manuscript under review and not accepte

Antifragility in Climbing:Determining Optimal Stress Loads for Athletic Performance Training

In the past decades, much research has examined the negative effects of stressors on the performance of athletes. However, according to evolutionary biology, organisms may exhibit growth under stress, a phenomenon called antifragility. For both coaches and their athletes, a key question is how to design training conditions to help athletes develop the kinds of physical, physiological, and behavioral adaptations underlying antifragility. An answer to this important question requires a better understanding of how individual athletes respond to stress or loads in the context of relevant sports tasks. In order to contribute to such understanding, the present study leverages a theoretical and methodological approach to generate individualized load–response profiles in the context of a climbing task. Climbers (n = 37) were asked to complete different bouldering (climbing) routes with increasing loading (i.e. difficulty). We quantified the behavioral responses of each individual athlete by mathematically combining two measures obtained for each route: (a) maximal performance (i.e. the percentage of the route that was completed) and (b) number of attempts required to achieve maximal performance. We mapped this composite response variable as a function of route difficulty. This procedure resulted in load–response curves that captured each athlete’s adaptability to stress, termed phenotypic plasticity (PP), specifically operationalized as the area under the generated curves. The results indicate individual load–response profiles (and by extension PP) for athletes who perform at similar maximum levels. We discuss how these profiles might be used by coaches to systematically select stress loads that may be ideally featured in performance training

Influenza activity in Europe during eight seasons (1999–2007): an evaluation of the indicators used to measure activity and an assessment of the timing, length and course of peak activity (spread) across Europe

<p>Abstract</p> <p>Background</p> <p>The European Influenza Surveillance Scheme (EISS) has collected clinical and virological data on influenza since 1996 in an increasing number of countries. The EISS dataset was used to characterise important epidemiological features of influenza activity in Europe during eight winters (1999–2007). The following questions were addressed: 1) are the sentinel clinical reports a good measure of influenza activity? 2) how long is a typical influenza season in Europe? 3) is there a west-east and/or south-north course of peak activity ('spread') of influenza in Europe?</p> <p>Methods</p> <p>Influenza activity was measured by collecting data from sentinel general practitioners (GPs) and reports by national reference laboratories. The sentinel reports were first evaluated by comparing them to the laboratory reports and were then used to assess the timing and spread of influenza activity across Europe during eight seasons.</p> <p>Results</p> <p>We found a good match between the clinical sentinel data and laboratory reports of influenza collected by sentinel physicians (overall match of 72% for +/- 1 week difference). We also found a moderate to good match between the clinical sentinel data and laboratory reports of influenza from non-sentinel sources (overall match of 60% for +/- 1 week). There were no statistically significant differences between countries using ILI (influenza-like illness) or ARI (acute respiratory disease) as case definition. When looking at the peak-weeks of clinical activity, the average length of an influenza season in Europe was 15.6 weeks (median 15 weeks; range 12–19 weeks). Plotting the peak weeks of clinical influenza activity reported by sentinel GPs against the longitude or latitude of each country indicated that there was a west-east spread of peak activity (spread) of influenza across Europe in four winters (2001–2002, 2002–2003, 2003–2004 and 2004–2005) and a south-north spread in three winters (2001–2002, 2004–2005 and 2006–2007).</p> <p>Conclusion</p> <p>We found that: 1) the clinical data reported by sentinel physicians is a valid indicator of influenza activity; 2) the length of influenza activity across the whole of Europe was surprisingly long, ranging from 12–19 weeks; 3) in 4 out of the 8 seasons, there was a west-east spread of influenza, in 3 seasons a south-north spread; not associated with type of dominant virus in those seasons.</p

matchms - processing and similarity evaluation of mass spectrometry data

Mass spectrometry data is at the heart of numerous applications in the biomedical and lifesciences. With growing use of high-throughput techniques, researchers need to analyze largerand more complex datasets. In particular through joint effort in the research community,fragmentation mass spectrometry datasets are growing in size and number. Platforms such asMassBank (Horai et al., 2010), GNPS (Wang et al., 2016) or MetaboLights (Haug et al., 2020)serve as an open-access hub for sharing of raw, processed, or annotated fragmentation massspectrometry data. Without suitable tools, however, exploitation of such datasets remainsoverly challenging. In particular, large collected datasets contain data acquired using differentinstruments and measurement conditions, and can further contain a significant fraction ofinconsistent, wrongly labeled, or incorrect metadata (annotations)

Oxygenated versus non-oxygenated flush out and storage of donor livers:An experimental study

Background: During donor organ procurement and subsequent static cold storage (SCS), hepatic adenosine triphosphate (ATP) levels are progressively depleted, which contributes to ischemia-reperfusion injury (IRI). We sought to investigate a simple approach to prevent ATP depletion and IRI using a porcine donation after circulatory death (DCD) liver reperfusion model. Methods: After 30 min warm ischemia, porcine livers were flushed via the portal vein with cold (4 degrees C) non-oxygenated University of Wisconsin (UW) preservation solution (n = 6, control group) or with oxygenated UW (n = 6, OxyFlush group). Livers were then subjected to 4 h SCS in non-oxygenated (control) or oxygenated (OxyFlush) UW, followed by 4 h normothermic reperfusion using whole blood. Hepatic ATP levels were compared, and hepatobiliary function and injury were assessed. Results: At the end of SCS, ATP was higher in the OxyFlush group compared to controls (delta ATP of +0.26 vs. -0.68 mu mol/g protein, p = 0.04). All livers produced bile and metabolized lactate, and there were no differences between the groups. Grafts in the OxyFlush group had lower blood glucose levels after reperfusion (p = 0.04). Biliary pH, glucose and bicarbonate were not different between the groups. Injury markers including liver transaminases, lactate dehydrogenase, malondialdehyde, cell-free DNA and flavin mononucleotide in the SCS solution and during reperfusion were also similar. Histological assessment of the parenchyma and bile ducts did not reveal differences between the groups. Conclusion: Oxygenated flush out and storage of DCD porcine livers prevents ATP depletion during ischemia, but this does not seem sufficient to mitigate early signs of IRI

Oseltamivir-resistant influenza A(H1N1)pdm09 virus in Dutch travellers returning from Spain, August 2012

Two Dutch travellers were infected with oseltamivirresistant influenza A(H1N1)pdm09 viruses with an H275Y neuraminidase substitution in early August 2012. Both cases were probably infected during separate holidays at the Catalonian coast (Spain). No epidemiological connection between the two cases was found, and neither of them was treated with oseltamivir before specimen collection. Genetic analysis of the neuraminidase gene revealed the presence of previously described permissive mutations that may increase the likelihood of such strains emerging and spreading widely