Precision requirements for interferometric gridding in the analysis of a 21 cm power spectrum

Context. Experiments that try to observe the 21 cm redshifted signals from the epoch of reionisation (EoR) using interferometric low-frequency instruments have stringent requirements on the processing accuracy. Aims. We analyse the accuracy of radio interferometric gridding of visibilities with the aim to quantify the power spectrum bias caused by gridding. We do this ultimately to determine the suitability of different imaging algorithms and gridding settings for an analysis of a 21 cm power spectrum. Methods. We simulated realistic Low-Frequency Array (LOFAR) data and constructed power spectra with convolutional gridding and w stacking, w projection, image-domain gridding, and without w correction. These were compared against data that were directly Fourier transformed. The influence of oversampling, kernel size, w-quantization, kernel windowing function, and image padding were quantified. The gridding excess power was measured with a foreground subtraction strategy, for which foregrounds were subtracted using Gaussian progress regression, as well as with a foreground avoidance strategy. Results. Constructing a power spectrum with a significantly lower bias than the expected EoR signals is possible with the methods we tested, but requires a kernel oversampling factor of at least 4000, and when w-correction is used, at least 500 w-quantization levels. These values are higher than typically used values for imaging, but they are computationally feasible. The kernel size and padding factor parameters are less crucial. Of the tested methods, image-domain gridding shows the highest accuracy with the lowest imaging time. Conclusions. LOFAR 21 cm power spectrum results are not affected by gridding. Image-domain gridding is overall the most suitable algorithm for 21 cm EoR power spectrum experiments, including for future analyses of data from the Square Kilometre Array (SKA) EoR. Nevertheless, convolutional gridding with tuned parameters results in sufficient accuracy for interferometric 21 cm EoR experiments. This also holds for w stacking for wide-field imaging. The w-projection algorithm is less suitable because of the requirements for kernel oversampling, and a faceting approach is unsuitable because it causes spatial discontinuities

Intramuscular tendon injury is not associated with an increased hamstring reinjury rate within 12 months after return to play

Background Acute hamstring injury that includes intramuscular tendon injury has been suggested to be associated with increased reinjury risk. These observations were based on a relatively small number of retrospectively analysed cases. Objective To determine whether intramuscular tendon injury is associated with higher reinjury rates in acute hamstring injury. Methods MRIs of 165 athletes with an acute hamstring injury were obtained within 5 days of injury. Treatment consisted of a standardised criteria-based rehabilitation programme. Standardised MRI parameters and intramuscular tendon injury, the latter subdivided into tendon disruption and waviness, were scored. We prospectively recorded reinjuries, defined as acute onset of posterior thigh pain in the same leg within 12 months after return to play. Results Participants were predominantly football players (72%). Sixty-four of 165 (39%) participants had an index injury with intramuscular hamstring tendon disruption, and waviness was present in 37 (22%). In total, there were 32 (19%) reinjuries. There was no significant difference (HR: 1.05, 95% CI 0.52 to 2.12, P=0.898) in reinjury rate between index injuries with intramuscular tendon disruption (n=13, 20%) and without tendon disruption (n=19, 20%). There was no significant difference in reinjury rate (X&(1)=0.031, P=0.861) between index injuries with presence of waviness (n=7, 19%) and without presence of waviness (n=25, 20%). Conclusion In athletes with an acute hamstring injury, intramuscular tendon injury was not associated with an increased reinjury rate within 12 months after return to play

Decreased functional connectivity of the insula within the salience network as an indicator for prospective insufficient response to antidepressants

Insufficient response to treatment is the main cause of prolonged suffering from major depressive disorder (MDD). Early identification of insufficient response could result in faster and more targeted treatment strategies to reduce suffering. We therefore explored whether baseline alterations within and between resting state functional connectivity networks could serve as markers of insufficient response to antidepressant treatment in two years of follow-up. We selected MDD patients (N = 17) from the NEtherlands Study of Depression and Anxiety (NESDA), who received ≥ two antidepressants, indicative for insufficient response, during the two year follow-up, a group of MDD patients who received only one antidepressant (N = 32) and a healthy control group (N = 19) matched on clinical characteristics and demographics. An independent component analysis (ICA) of baseline resting-state scans was conducted after which functional connectivity within the components was compared between groups. We observed lower connectivity of the right insula within the salience network in the group with ≥ two antidepressants compared to the group with one antidepressant. No difference in connectivity was found between the patient groups and healthy control group. Given the suggested role of the right insula in switching between task-positive mode (activation during attention-demanding tasks) and task-negative mode (activation during the absence of any task), we explored whether right insula activation differed during switching between these two modes. We observed that in the ≥2 antidepressant group, the right insula was less active compared to the group with one antidepressant, when switching from task-positive to task-negative mode than the other way around. These findings imply that lower right insula connectivity within the salience network may serve as an indicator for prospective insufficient response to antidepressants. This result, supplemented by the diminished insula activation when switching between task and rest related networks, could indicate an underlying mechanism that, if not sufficiently targeted by current antidepressants, could lead to insufficient response. When replicated, these findings may contribute to the identification of biomarkers for early detection of insufficient response

Least Upper Delay Bound for VBR Flows in Networks-on- Chip with Virtual Channels

Real-time applications such as multimedia and gaming require stringent performance guarantees, usually enforced by a tight upper bound on the maximum end-to-end delay. For FIFO multiplexed on-chip packet switched networks we consider worst-case delay bounds for Variable Bit-Rate (VBR) flows with aggregate scheduling, which schedules multiple flows as an aggregate flow. VBR Flows are characterized by a maximum transfer size, peak rate, burstiness, and average sustainable rate. Based on network calculus, we present and prove theorems to derive per-flow end-to-end Equivalent Service Curves (ESC) which are in turn used for computing Least Upper Delay Bounds (LUDBs) of individual flows. In a realistic case study we find that the end-to-end delay bound is up to 46.9% more accurate than the case without considering the traffic peak behavior. Likewise, results also show similar improvements for synthetic traffic patterns. The proposed methodology is implemented in C++ and has low run-time complexity, enabling quick evaluation for large and complex SoCs

Gastrointestinal ulceration as a possible side effect of bevacizumab which may herald perforation

Chemotherapy plus bevacizumab is currently considered as the standard 1st line treatment of advanced colorectal cancer (ACC). Whereas GI perforation is a known side effect of bevacizumab, the development of GI ulcers has not been reported. We identified 18 patients with ACC who participated in a phase III multicentre trial which included chemotherapy and bevacizumab, who developed a GI ulcer (n = 6), perforation (n = 8) or both (n = 4). The risk of developing a symptomatic GI ulcer or perforation was 1.3% and 1.6%, respectively. Central review of the histology specimens showed ulceration and/or granulation tissue with neovascularisation. The majority (89%) of events developed early during treatment. Given these observations, as well as the relationship between VEGF and mucosal injury healing, we suggest that GI ulcers may occur as a side effect of treatment with bevacizumab and may herald perforation

First LOFAR observations at very low frequencies of cluster-scale non-thermal emission: the case of Abell 2256

Abell 2256 is one of the best known examples of a galaxy cluster hosting large-scale diffuse radio emission that is unrelated to individual galaxies. It contains both a giant radio halo and a relic, as well as a number of head-tail sources and smaller diffuse steep-spectrum radio sources. The origin of radio halos and relics is still being debated, but over the last years it has become clear that the presence of these radio sources is closely related to galaxy cluster merger events. Here we present the results from the first LOFAR Low band antenna (LBA) observations of Abell 2256 between 18 and 67 MHz. To our knowledge, the image presented in this paper at 63 MHz is the deepest ever obtained at frequencies below 100 MHz in general. Both the radio halo and the giant relic are detected in the image at 63 MHz, and the diffuse radio emission remains visible at frequencies as low as 20 MHz. The observations confirm the presence of a previously claimed ultra-steep spectrum source to the west of the cluster center with a spectral index of -2.3 \pm 0.4 between 63 and 153 MHz. The steep spectrum suggests that this source is an old part of a head-tail radio source in the cluster. For the radio relic we find an integrated spectral index of -0.81 \pm 0.03, after removing the flux contribution from the other sources. This is relatively flat which could indicate that the efficiency of particle acceleration at the shock substantially changed in the last \sim 0.1 Gyr due to an increase of the shock Mach number. In an alternative scenario, particles are re-accelerated by some mechanism in the downstream region of the shock, resulting in the relatively flat integrated radio spectrum. In the radio halo region we find indications of low-frequency spectral steepening which may suggest that relativistic particles are accelerated in a rather inhomogeneous turbulent region.Comment: 13 pages, 13 figures, accepted for publication in A\&A on April 12, 201

Analytical performance of a PCR assay for the detection of KRAS mutations (codons 12/13 and 61) in formalin-fixed paraffin-embedded tissue samples of colorectal carcinoma

KRAS mutation testing is mandatory before prescribing anti-epidermal growth factor monoclonal antibodies in the treatment of advanced colorectal cancer. We describe the performance of a TaqMelt polymerase chain reaction (PCR) assay—the cobas® KRAS Mutation Test—designed to detect 19 mutations in codons 12, 13, and 61. The limit of detection was determined using DNA blends from cell lines, plasmids, and formalin-fixed paraffin-embedded tissue specimens. Assay performance was compared to Sanger sequencing using a panel of 188 specimens. Discordant specimens were subjected to next generation pyrosequencing (454). Assay repeatability was assessed using a panel of six specimens. A >95% correct mutation call rate was obtained in all specimen types with ~5% mutant alleles at DNA inputs of 0.8–6.3 ng per PCR reaction; 100% detection rate was observed at the recommended DNA input of 50 ng. The positive percent agreement with Sanger was 97.5% (79/81) for codons 12/13 and 85.7% (6/7) for codon 61. Negative percent agreement was 94.4% (101/107) for codon 12/13 and 99.4% (180/181) for codon 61. Nine of 10 discordant specimens yielded 454 results consistent with the cobas® results. With repeated testing, the assay showed a correct call rate of 100% (192/192) for all operators, instruments, reagent lots, and days tested. The cobas® test detects KRAS mutations in codons 12, 13, and 61 at a limit of detection of <5%. The PCR assay was more sensitive and specific than Sanger sequencing, and performance was highly reproducible. Test performance was not influenced by various endogenous interfering substances or common gut microbes