A Giant Sample of Giant Pulses from the Crab Pulsar

We observed the Crab pulsar with the 43-m telescope in Green Bank, WV over a timespan of 15 months. In total we obtained 100 hours of data at 1.2 GHz and seven hours at 330 MHz, resulting in a sample of about 95000 giant pulses (GPs). This is the largest sample, to date, of GPs from the Crab pulsar taken with the same telescope and backend and analyzed as one data set. We calculated power-law fits to amplitude distributions for main pulse (MP) and interpulse (IP) GPs, resulting in indices in the range of 2.1-3.1 for MP GPs at 1.2 GHz and in the range of 2.5-3.0 and 2.4-3.1 for MP and IP GPs at 330 MHz. We also correlated the GPs at 1.2 GHz with GPs from the Robert C. Byrd Green Bank Telescope (GBT), which were obtained simultaneously at a higher frequency (8.9 GHz) over a span of 26 hours. In total, 7933 GPs from the 43-m telescope at 1.2 GHz and 39900 GPs from the GBT were recorded during these contemporaneous observations. At 1.2 GHz, 236 (3%) MP GPs and 23 (5%) IP GPs were detected at 8.9 GHz, both with zero chance probability. Another 15 (4%) low-frequency IP GPs were detected within one spin period of high-frequency IP GPs, with a chance probability of 9%. This indicates that the emission processes at high and low radio frequencies are related, despite significant pulse profile shape differences. The 43-m GPs were also correlated with Fermi gamma-ray photons to see if increased pair production in the magnetosphere is the mechanism responsible for GP emission. A total of 92022 GPs and 393 gamma-ray photons were used in this correlation analysis. No significant correlations were found between GPs and gamma-ray photons. This indicates that increased pair production in the magnetosphere is likely not the dominant cause of GPs. Possible methods of GP production may be increased coherence of synchrotron emission or changes in beaming direction.Comment: 33 pages, 10 figures, 6 tables, accepted for publication in Ap

Does mode of administration affect health-related quality-of-life outcomes after stroke?

Telephone interviews and postal surveys may be a resource-efficient way of assessing health-related quality-of-life post-stroke, if they produce data equivalent to face-to-face interviews. This study explored whether telephone interviews and postal surveys of the Stroke and Aphasia Quality of Life Scale (SAQOL-39g) yielded similar results to face-to-face interviews. Participants included people with aphasia and comprised two groups: group one (n =22) were 3-6 months post-stroke; group two (n =26) were ≥1 year post-stroke. They completed either a face-to-face and a telephone interview or a face-to-face interview and a postal survey of the SAQOL-39g. Response rates were higher for group two (87%) than for group one (72-77%). There were no significant differences between respondents and non-respondents on demographics, co-morbidities, stroke severity, or communication impairment. Concordance between face-to-face and telephone administrations (.90-.98) was excellent; and very good-excellent between face-to-face and postal administrations (.84-.96), although scores in postal administrations were lower (significant for psychosocial domain and overall SAQOL-39g in group two). These findings suggest that the SAQOL-39g yields similar results in different modes of administration. Researchers and clinicians may employ alternative modes, particularly in the longer term post-stroke, in order to reduce costs or facilitate clients with access difficulties

Dynamical Fermions with Fat Links

We present and test a new method for simulating dynamical fermions with fat links. Our construction is based on the introduction of auxiliary but dynamical gauge fields and works with any fermionic action and can be combined with any fermionic updating. In our simulation we use an over-relaxation step which makes it effective. For four flavors of staggered fermions first results indicate that flavor symmetry at a lattice spacing a~0.2 fm is restored to a few percent. With the standard action this amount of flavor symmetry restoration is achieved at a~0.07 fm. We estimate that the overall computational cost is reduced by at least a factor 10.Comment: 11 pages, 4 figures, detailed description of over-relaxation and references added, figures with more statistic

A biophysical model of prokaryotic diversity in geothermal hot springs

Recent field investigations of photosynthetic bacteria living in geothermal hot spring environments have revealed surprisingly complex ecosystems, with an unexpected level of genetic diversity. One case of particular interest involves the distribution along hot spring thermal gradients of genetically distinct bacterial strains that differ in their preferred temperatures for reproduction and photosynthesis. In such systems, a single variable, temperature, defines the relevant environmental variation. In spite of this, each region along the thermal gradient exhibits multiple strains of photosynthetic bacteria adapted to several distinct thermal optima, rather than the expected single thermal strain adapted to the local environmental temperature. Here we analyze microbiology data from several ecological studies to show that the thermal distribution field data exhibit several universal features independent of location and specific bacterial strain. These include the distribution of optimal temperatures of different thermal strains and the functional dependence of the net population density on temperature. Further, we present a simple population dynamics model of these systems that is highly constrained by biophysical data and by physical features of the environment. This model can explain in detail the observed diversity of different strains of the photosynthetic bacteria. It also reproduces the observed thermal population distributions, as well as certain features of population dynamics observed in laboratory studies of the same organisms

PET Reconstruction With an Anatomical MRI Prior Using Parallel Level Sets.

The combination of positron emission tomography (PET) and magnetic resonance imaging (MRI) offers unique possibilities. In this paper we aim to exploit the high spatial resolution of MRI to enhance the reconstruction of simultaneously acquired PET data. We propose a new prior to incorporate structural side information into a maximum a posteriori reconstruction. The new prior combines the strengths of previously proposed priors for the same problem: it is very efficient in guiding the reconstruction at edges available from the side information and it reduces locally to edge-preserving total variation in the degenerate case when no structural information is available. In addition, this prior is segmentation-free, convex and no a priori assumptions are made on the correlation of edge directions of the PET and MRI images. We present results for a simulated brain phantom and for real data acquired by the Siemens Biograph mMR for a hardware phantom and a clinical scan. The results from simulations show that the new prior has a better trade-off between enhancing common anatomical boundaries and preserving unique features than several other priors. Moreover, it has a better mean absolute bias-to-mean standard deviation trade-off and yields reconstructions with superior relative l2-error and structural similarity index. These findings are underpinned by the real data results from a hardware phantom and a clinical patient confirming that the new prior is capable of promoting well-defined anatomical boundaries.This research was funded by the EPSRC (EP/K005278/1) and EP/H046410/1 and supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre. M.J.E was supported by an IMPACT studentship funded jointly by Siemens and the UCL Faculty of Engineering Sciences. K.T. and D.A. are partially supported by the EPSRC grant EP/M022587/1.This is the author accepted manuscript. The final version is available from IEEE via http://dx.doi.org/10.1109/TMI.2016.254960

Identifying epileptogenic abnormalities through spatial clustering of MEG interictal band power

Successful epilepsy surgery depends on localising and resecting cerebral abnormalities and networks that generate seizures. Abnormalities, however, may be widely distributed across multiple discontiguous areas. We propose spatially constrained clusters as candidate areas for further investigation, and potential resection. We quantified the spatial overlap between the abnormality cluster and subsequent resection, hypothesising a greater overlap in seizure-free patients. Thirty-four individuals with refractory focal epilepsy underwent pre-surgical resting-state interictal MEG recording. Fourteen individuals were totally seizure free (ILAE 1) after surgery and 20 continued to have some seizures post-operatively (ILAE 2+). Band power abnormality maps were derived using controls as a baseline. Patient abnormalities were spatially clustered using the k-means algorithm. The tissue within the cluster containing the most abnormal region was compared with the resection volume using the dice score. The proposed abnormality cluster overlapped with the resection in 71% of ILAE 1 patients. Conversely, an overlap only occurred in 15% of ILAE 2+ patients. This effect discriminated outcome groups well (AUC=0.82). Our novel approach identifies clusters of spatially similar tissue with high abnormality. This is clinically valuable, providing (i) a data-driven framework to validate current hypotheses of the epileptogenic zone localisation or (ii) to guide further investigation.Comment: 16 pages, 3 figure

Epistasis dominates the genetic architecture of Drosophila quantitative traits

Epistasis-nonlinear genetic interactions between polymorphic loci-is the genetic basis of canalization and speciation, and epistatic interactions can be used to infer genetic networks affecting quantitative traits. However, the role that epistasis plays in the genetic architecture of quantitative traits is controversial. Here, we compared the genetic architecture of three Drosophila life history traits in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and a large outbred, advanced intercross population derived from 40 DGRP lines (Flyland). We assessed allele frequency changes between pools of individuals at the extremes of the distribution for each trait in the Flyland population by deep DNA sequencing. The genetic architecture of all traits was highly polygenic in both analyses. Surprisingly, none of the SNPs associated with the traits in Flyland replicated in the DGRP and vice versa. However, the majority of these SNPs participated in at least one epistatic interaction in the DGRP. Despite apparent additive effects at largely distinct loci in the two populations, the epistatic interactions perturbed common, biologically plausible, and highly connected genetic networks. Our analysis underscores the importance of epistasis as a principal factor that determines variation for quantitative traits and provides a means to uncover genetic networks affecting these traits. Knowledge of epistatic networks will contribute to our understanding of the genetic basis of evolutionarily and clinically important traits and enhance predictive ability at an individualized level in medicine and agricultur

MEG abnormalities and mechanisms of surgical failure in neocortical epilepsy

Objective: Epilepsy surgery fails to achieve seizure freedom in 30%–40% of cases. It is not fully understood why some surgeries are unsuccessful. By comparing interictal magnetoencephalography (MEG) band power from patient data to normative maps, which describe healthy spatial and population variability, we identify patient-specific abnormalities relating to surgical failure. We propose three mechanisms contributing to poor surgical outcome: (1) not resecting the epileptogenic abnormalities (mislocalization), (2) failing to remove all epileptogenic abnormalities (partial resection), and (3) insufficiently impacting the overall cortical abnormality. Herein we develop markers of these mechanisms, validating them against patient outcomes. Methods: Resting-state MEG recordings were acquired for 70 healthy controls and 32 patients with refractory neocortical epilepsy. Relative band-power spatial maps were computed using source-localized recordings. Patient and region-specific band-power abnormalities were estimated as the maximum absolute z-score across five frequency bands using healthy data as a baseline. Resected regions were identified using postoperative magnetic resonance imaging (MRI). We hypothesized that our mechanistically interpretable markers would discriminate patients with and without postoperative seizure freedom. Results: Our markers discriminated surgical outcome groups (abnormalities not targeted: area under the curve [AUC] = 0.80, p = .003; partial resection of epileptogenic zone: AUC = 0.68, p = .053; and insufficient cortical abnormality impact: AUC = 0.64, p = .096). Furthermore, 95% of those patients who were not seizure-free had markers of surgical failure for at least one of the three proposed mechanisms. In contrast, of those patients without markers for any mechanism, 80% were ultimately seizure-free. Significance: The mapping of abnormalities across the brain is important for a wide range of neurological conditions. Here we have demonstrated that interictal MEG band-power mapping has merit for the localization of pathology and improving our mechanistic understanding of epilepsy. Our markers for mechanisms of surgical failure could be used in the future to construct predictive models of surgical outcome, aiding clinical teams during patient pre-surgical evaluations

Identifying epileptogenic abnormalities through spatial clustering of MEG interictal band power

Successful epilepsy surgery depends on localising and resecting cerebral abnormalities and networks that generate seizures. Abnormalities, however, may be widely distributed across multiple discontiguous areas. We propose spatially constrained clusters as candidate areas for further investigation, and potential resection. We quantified the spatial overlap between the abnormality cluster and subsequent resection, hypothesising a greater overlap in seizure-free patients. Thirty-four individuals with refractory focal epilepsy underwent pre-surgical resting-state interictal MEG recording. Fourteen individuals were totally seizure free (ILAE 1) after surgery and 20 continued to have some seizures post-operatively (ILAE 2+). Band power abnormality maps were derived using controls as a baseline. Patient abnormalities were spatially clustered using the k-means algorithm. The tissue within the cluster containing the most abnormal region was compared with the resection volume using the dice score. The proposed abnormality cluster overlapped with the resection in 71% of ILAE 1 patients. Conversely, an overlap only occurred in 15% of ILAE 2+ patients. This effect discriminated outcome groups well (AUC=0.82). Our novel approach identifies clusters of spatially similar tissue with high abnormality. This is clinically valuable, providing (i) a data-driven framework to validate current hypotheses of the epileptogenic zone localisation or (ii) to guide further investigation