pulsar_spectra: A pulsar flux density catalogue and spectrum fitting repository

We present the pulsar_spectra software repository, an open-source pulsar flux density catalogue and automated spectral fitting software that finds the best spectral model and produces publication-quality plots. The Python-based software includes features that enable users in the astronomical community to add newly published spectral measurements to the catalogue as they become available. The spectral fitting software is an implementation of the method described in Jankowski et al. (2018) which uses robust statistical methods to decide on the best-fitting model for individual pulsar spectra. pulsar_spectra is motivated by the need for a centralised repository for pulsar flux density measurements to make published measurements more accessible to the astronomical community and provide a suite of tools for measuring spectra

An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ(TM)

BACKGROUND: Proteomics continues to play a critical role in post-genomic science as continued advances in mass spectrometry and analytical chemistry support the separation and identification of increasing numbers of peptides and proteins from their characteristic mass spectra. In order to facilitate the sharing of this data, various standard formats have been, and continue to be, developed. Still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic technologies that are being developed. RESULTS: We propose an extension to the PRIDE and mzData XML schema to accommodate the concept of multiple samples per experiment, and in addition, capture the intensities of the iTRAQ(TM )reporter ions in the entry. A simple Java-client has been developed to capture and convert the raw data from common spectral file formats, which also uses a third-party open source tool for the generation of iTRAQ(TM) reported intensities from Mascot output, into a valid PRIDE XML entry. CONCLUSION: We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQ(TM) data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from

MWA Tied-Array Processing IV: A Multi-Pixel Beamformer for Pulsar Surveys and Ionospheric Corrected Localisation

The Murchison Widefield Array (MWA) is a low-frequency aperture array capable of high-time and frequency resolution astronomy applications such as pulsar studies. The large field-of-view of the MWA (hundreds of square degrees) can also be exploited to attain fast survey speeds for all-sky pulsar search applications, but to maximise sensitivity requires forming thousands of tied-array beams from each voltage-capture observation. The necessity of using calibration solutions that are separated from the target observation both temporally and spatially makes pulsar observations vulnerable to uncorrected, frequency-dependent positional offsets due to the ionosphere. These offsets may be large enough to move the source away from the centre of the tied-array beam, incurring sensitivity drops of $\sim$30-50\% in Phase II extended array configuration. We analyse these offsets in pulsar observations and develop a method for mitigating them, improving both the source position accuracy and the sensitivity. This analysis prompted the development of a multi-pixel beamforming functionality that can generate dozens of tied-array beams simultaneously, which runs a factor of ten times faster compared to the original single-pixel version. This enhancement makes it feasible to observe multiple pulsars within the vast field of view of the MWA and supports the ongoing large-scale pulsar survey efforts with the MWA. We explore the extent to which ionospheric offset correction will be necessary for the MWA Phase III and the low-frequency Square Kilometre Array (SKA-Low).Comment: 10 pages, 5 figure

A targeted search for repeating fast radio bursts with the MWA

We present a targeted search for low-frequency (144--215\,MHz) FRB emission from five repeating FRBs using 23.3\,hr of archival data taken with the Murchison Widefield Array (MWA) Voltage Capture System (VCS) between 2014 September and 2020 May. This is the first time that the MWA VCS has been used to search for FRB signals from known repeaters, which enables much more sensitive FRB searches than previously performed with the standard MWA correlator mode. We performed a standard single pulse search with a temporal and spectral resolution of $400\,\mu$s and 10\,kHz, respectively, over a $100\,\text{pc}\,\text{cm}^{-3}$ dispersion measure (DM) range centred at the known DM of each studied repeating FRB. No FRBs exceeding a $6\sigma$ threshold were detected. The fluence upper limits in the range of 32--1175\,Jy\,ms and 36--488\,Jy\,ms derived from 10 observations of FRB 20190711A and four observations of FRB 20201124A respectively, allow us to constrain the spectral indices of their bursts to $\gtrsim-1$ if these two repeaters were active during the MWA observations. If free-free absorption is responsible for our non-detection, we can constrain the size of the absorbing medium in terms of the electron temperature $T$ to $<1.00\times(T/10^4\text{K})^{-1.35}\,\text{pc}$, $<0.92\times(T/10^4\text{K})^{-1.35}\,\text{pc}$ and $<[0.22\text{--}2.50]\times(T/10^4\text{K})^{-1.35}\,\text{pc}$ for FRB 20190117A, 20190711A, and 20201124A, respectively. However, given that the activities of these repeaters are not well characterised, our non-detections could also suggest they were inactive during the MWA observations.Comment: Accepted for publication in MNRA

Recon 2.2: from reconstruction to model of human metabolism.

IntroductionThe human genome-scale metabolic reconstruction details all known metabolic reactions occurring in humans, and thereby holds substantial promise for studying complex diseases and phenotypes. Capturing the whole human metabolic reconstruction is an on-going task and since the last community effort generated a consensus reconstruction, several updates have been developed.ObjectivesWe report a new consensus version, Recon 2.2, which integrates various alternative versions with significant additional updates. In addition to re-establishing a consensus reconstruction, further key objectives included providing more comprehensive annotation of metabolites and genes, ensuring full mass and charge balance in all reactions, and developing a model that correctly predicts ATP production on a range of carbon sources.MethodsRecon 2.2 has been developed through a combination of manual curation and automated error checking. Specific and significant manual updates include a respecification of fatty acid metabolism, oxidative phosphorylation and a coupling of the electron transport chain to ATP synthase activity. All metabolites have definitive chemical formulae and charges specified, and these are used to ensure full mass and charge reaction balancing through an automated linear programming approach. Additionally, improved integration with transcriptomics and proteomics data has been facilitated with the updated curation of relationships between genes, proteins and reactions.ResultsRecon 2.2 now represents the most predictive model of human metabolism to date as demonstrated here. Extensive manual curation has increased the reconstruction size to 5324 metabolites, 7785 reactions and 1675 associated genes, which now are mapped to a single standard. The focus upon mass and charge balancing of all reactions, along with better representation of energy generation, has produced a flux model that correctly predicts ATP yield on different carbon sources.ConclusionThrough these updates we have achieved the most complete and best annotated consensus human metabolic reconstruction available, thereby increasing the ability of this resource to provide novel insights into normal and disease states in human. The model is freely available from the Biomodels database (http://identifiers.org/biomodels.db/MODEL1603150001)

Independent discovery of a nulling pulsar with unusual subpulse drifting properties with the Murchison Widefield Array

We report the independent discovery of PSR J0026-1955 with the Murchison Widefield Array (MWA) in the ongoing Southern-sky MWA Rapid Two-metre pulsar survey. J0026-1955 has a period of ∼1.306 s, a dispersion measure of ∼20.869 pc cm-3, and a nulling fraction of ∼77%. This pulsar highlights the advantages of the survey's long dwell times (∼80 minutes), which, when fully searched, will be sensitive to the expected population of similarly bright, intermittent pulsars with long nulls. A single-pulse analysis in the MWA's 140-170 MHz band also reveals a complex subpulse drifting behavior, including both rapid changes of the drift rate characteristic of mode switching pulsars, as well as a slow, consistent evolution of the drift rate within modes. In some longer drift sequences, interruptions in the otherwise smooth drift rate evolution occur preferentially at a particular phase, typically lasting a few pulses. These properties make this pulsar an ideal test bed for prevailing models of drifting behavior such as the carousel model