A data analysis library for gravitational wave detection

One of the main goals of Pulsar Timing Arrays (PTAs) is the direct detection of gravitational waves (GWs). A first detection will be a major leap for astronomy and substantial effort is currently going into timing as many pulsars as possible, with the highest possible accuracy. As part of the individual PTA projects, several groups are developing data analysis methods for the final stage of a gravitational-waves search pipeline: the analysis of the timing residuals. Here we report the progress of on-going work to develop, within a Bayesian framework, a comprehensive and user friendly analysis library to search for gravitational waves in PTA data

Analysis of the first IPTA Mock Data Challenge by the EPTA timing data analysis working group

This is a summary of the methods we used to analyse the first IPTA Mock Data Challenge (MDC), and the obtained results. We have used a Bayesian analysis in the time domain, accelerated using the recently developed ABC-method which consists of a form of lossy linear data compression. The TOAs were first processed with Tempo2, where the design matrix was extracted for use in a subsequent Bayesian analysis. We used different noise models to analyse the datasets: no red noise, red noise the same for all pulsars, and individual red noise per pulsar. We sampled from the likelihood with four different samplers: "emcee", "t-walk", "Metropolis-Hastings", and "pyMultiNest". All but emcee agreed on the final result, with emcee failing due to artefacts of the high-dimensionality of the problem. An interesting issue we ran into was that the prior of all the 36 (red) noise amplitudes strongly affects the results. A flat prior in the noise amplitude biases the inferred GWB amplitude, whereas a flat prior in log-amplitude seems to work well. This issue is only apparent when using a noise model with individually modelled red noise for all pulsars. Our results for the blind challenges are in good agreement with the injected values. For the GWB amplitudes we found h_c = 1.03 +/- 0.11 [10^{-14}], h_c = 5.70 +/- 0.35 [10^{-14}], and h_c = 6.91 +/- 1.72 [10^{-15}], and for the GWB spectral index we found gamma = 4.28 +/- 0.20, gamma = 4.35 +/- 0.09, and gamma = 3.75 +/- 0.40. We note that for closed challenge 3 there was quite some covariance between the signal and the red noise: if we constrain the GWB spectral index to the usual choice of gamma = 13/3, we obtain the estimates: h_c = 10.0 +/- 0.64 [10^{-15}], h_c = 56.3 +/- 2.42 [10^{-15}], and h_c = 4.83 +/- 0.50 [10^{-15}], with one-sided 2 sigma upper-limits of: h_c <= 10.98 [10^{-15}], h_c <= 60.29 [10^{-15}], and h_c <= 5.65 [10^{-15}]

Nine years of experimental warming did not influence the thermal sensitivity of metabolic rate in the medaka fish Oryzias latipes

A pressing challenge is to determine whether and how global-change drivers influence species physiology and survival. Recently, researchers have proposed the metabolic theory of ecology, defending the hypothesis of a universal thermal dependence of metabolic rate or, alternatively, the metabolic cold adaptation theory, stating that local adaptation can influence the thermal sensitivity of metabolic rate. However, the long-term (i.e. multigenerational) consequences of warming for the thermal sensitivity of metabolic rate remain largely unexplored although it determines energy use and is crucial for species response to climate change. In this study, we used an evolutionary experiment with medaka fishes Oryzias latipes maintained for more than 12 generations at warm and cold temperatures (30 and 20°C, respectively) to address this issue. Our objective was to investigate whether thermal adaptation influences the relationship between temperature and mass-corrected metabolic rate and how this may occur. In agreement with the universal thermal dependence hypothesis, we found that warming did not significantly influence the thermal sensitivity of mass-corrected metabolic rate: neither the intercept nor the slope of the temperature–metabolic rate relationship differed among fish lineages. Our small-scale laboratory experiment thus indicated that there is limited potential for evolutionary change in medaka fish metabolic rate in response to warmer temperatures. Overall, we provide evidence that 9 years of experimental warming did not influence the thermal sensitivity of metabolic rate. Our results highlight the invariability of the thermal dependence of metabolic rate, which has important implications for adaptation to climate warming. This finding suggests a limited potential for metabolic adaptations in response to long-term temperature changes, which may have negative consequences for the persistence of fish populations under climate change

Phenotypic responses of invasive species to removals affect ecosystem functioning and restoration.

Reducing the abundances of invasive species by removals aims to minimize their ecological impacts and enable ecosystem recovery. Removal methods are usually selective, modifying phenotypic traits in the managed populations. However, there is little empirical evidence of how removal-driven changes in multiple phenotypic traits of surviving individuals of invasive species can affect ecosystem functioning and recovery. Overcoming this knowledge gap is highly relevant because individuals are the elemental units of ecological processes and so integrating individual-level responses into the management of biological invasions could improve their efficiency. Here we provide novel demonstration that removals by trapping, angling and biocontrol from lakes of the globally invasive crayfish Procambarus clarkii induced substantial changes in multiple phenotypic traits. A mesocosm experiment then revealed that these changes in phenotypic traits constrain recovery of basic ecosystem functions (decomposition of organic matter, benthic primary production) by acting in the opposite direction than the effects of reduced invader abundance. However, only minor ecological impacts of invader abundance and phenotypic traits variation remained a year after its complete eradication. Our study provides quantitative evidence to an original idea that removal-driven trait changes can dampen recovery of invaded ecosystems even when the abundance of invasive species is substantially reduced. We suggest that the phenotypic responses of invaders to the removal programme have strong effects on ecosystem recovery and should be considered within the management of biological invasions, particularly when complete eradication is not achievable

Long-term quality of life after surgery of head and neck cancer with microvascular reconstruction : a prospective study with 4.9-years follow-up

Purpose The aim of this study was to evaluate the long-term health-related quality of life (HRQoL) of head and neck cancer patients with microvascular surgery. Surgical treatment causes great changes in patient HRQoL. Studies focusing on long-term HRQoL after microvascular reconstruction for head and neck cancer patients are scarce. Methods We conducted a prospective study of 93 patients with head and neck cancer and microvascular reconstruction in Helsinki University Hospital Finland. HRQoL was measured using the 15D instrument at baseline and after a mean 4.9-years follow up. Results were compared with those of an age-standardized general population. Results Of the 93 patients, 61 (66%) were alive after follow-up; of these, 42 (69%) answered the follow-up questionnaire. The median time between surgery and HRQoL assessment was 4.9 years (range 3.7-7.8 years). The mean 15D score of all patients (n = 42) at the 4.9-years follow up was statistically significantly (p = 0.010) and clinically importantly lower than at baseline. The dimensions of "speech" and "usual activities" were significantly impaired at the end of follow up. There was a significant difference at the 4.9-years follow-up in the mean 15D score between patients and the general population (p = 0.014). After follow up, patients were significantly (p <0.05) worse off on the dimensions of "speech," "eating," and "usual activities." Conclusions Long-term HRQoL was significantly reduced in the whole patient cohort. Speech and usual activities were the most affected dimensions in head and neck cancer patients with microvascular reconstruction at the end of the 4.9-years follow up.Peer reviewe

Laboratory captivity can affect scores of metabolic rates and activity in wild brown trout

Phenotypic scoring of wild animals under standardized laboratory conditions is important as it allows field ecologists and evolutionary biologists to understand the development and maintenance of interindividual differences in plastic traits (e.g. behaviour and physiology). However, captivity is associated with a shift from a natural familiar environment to an unfamiliar and artificial environment, which may affect estimates of plastic phenotypic traits. In this study, we tested how previous experience with laboratory environments and time spent in captivity affects behavioural (i.e. activity) and metabolic (i.e. standard and maximum metabolic rates) scoring of our model species, wild brown trout Salmo trutta. We found that individuals with previous experience of laboratory captivity (10.5 months earlier) showed higher activity in an open field test than individuals with no prior experience of laboratory captivity. Previous experience with captivity had no significant effect on metabolic rates. However, metabolic rates seemed to increase with increasing time spent in captivity prior to the collection of measurements. Although there are benefits of keeping wild animals in captivity prior to scoring, our results suggest that while allowing for sufficient acclimatization researchers should aim at minimizing time in captivity of wild animals to increase accuracy and ecological relevance of the scoring of plastic phenotypic traits

The noise properties of 42 millisecond pulsars from the European Pulsar Timing Array and their impact on gravitational wave searches

The sensitivity of Pulsar Timing Arrays to gravitational waves depends on the noise present in the individual pulsar timing data. Noise may be either intrinsic or extrinsic to the pulsar. Intrinsic sources of noise will include rotational instabilities, for example. Extrinsic sources of noise include contributions from physical processes which are not sufficiently well modelled, for example, dispersion and scattering effects, analysis errors and instrumental instabilities. We present the results from a noise analysis for 42 millisecond pulsars (MSPs) observed with the European Pulsar Timing Array. For characterising the low-frequency, stochastic and achromatic noise component, or "timing noise", we employ two methods, based on Bayesian and frequentist statistics. For 25 MSPs, we achieve statistically significant measurements of their timing noise parameters and find that the two methods give consistent results. For the remaining 17 MSPs, we place upper limits on the timing noise amplitude at the 95% confidence level. We additionally place an upper limit on the contribution to the pulsar noise budget from errors in the reference terrestrial time standards (below 1%), and we find evidence for a noise component which is present only in the data of one of the four used telescopes. Finally, we estimate that the timing noise of individual pulsars reduces the sensitivity of this data set to an isotropic, stochastic GW background by a factor of >9.1 and by a factor of >2.3 for continuous GWs from resolvable, inspiralling supermassive black-hole binaries with circular orbits.Comment: Accepted for publication by the Monthly Notices of the Royal Astronomical Societ

P62 accumulates through neuroanatomical circuits in response to tauopathy propagation

In Alzheimer's disease and related tauopathies, trans-synaptic transfer and accumulation of pathological tau from donor to recipient neurons is thought to contribute to disease progression, but the underlying mechanisms are poorly understood. Using complementary in vivo and in vitro models, we examined the relationship between these two processes and neuronal clearance. Accumulation of p62 (a marker of defective protein clearance) correlated with pathological tau accumulation in two mouse models of tauopathy spread; Entorhinal Cortex-tau (EC-Tau) mice where tau pathology progresses in time from EC to other brain regions, and PS19 mice injected with tau seeds. In both models and in several brain regions, p62 colocalized with human tau in a pathological conformation (MC1 antibody). In EC-Tau mice, p62 accumulated before overt tau pathology had developed and was associated with the presence of aggregation-competent tau seeds identified using a FRET-based assay. Furthermore, p62 accumulated in the cytoplasm of neurons in the dentate gyrus of EC-Tau mice prior to the appearance of MC1 positive tauopathy. However, MC1 positive tau was shown to be present at the synapse and to colocalize with p62 as shown by immuno electron microscopy. In vitro, p62 colocalized with tau inclusions in two primary cortical neuron models of tau pathology. In a three-chamber microfluidic device containing neurons overexpressing fluorescent tau, seeding of tau in the donor chamber led to tau pathology spread and p62 accumulation in both the donor and the recipient chamber. Overall, these data are in accordance with the hypothesis that the accumulation and trans-synaptic spread of pathological tau disrupts clearance mechanisms, preceding the appearance of obvious tau aggregation. A vicious cycle of tau accumulation and clearance deficit would be expected to feed-forward and exacerbate disease progression across neuronal circuits in human tauopathies