The microbiological profile of necrotising fasciitis at a secondary level hospital in Gauteng

Background: Necrotising fasciitis (NF) is a fulminant soft tissue infection that requires timely diagnosis, urgent surgical debridement, and appropriate antimicrobial therapy. The choice of empiric antimicrobial therapy depends on the microorganisms cultured and the antimicrobial resistance profile of the institution. Necrotising fasciitis has not been studied in our setting. Objectives: The aim of the study was to audit the microbiological profile of NF and antimicrobial susceptibility profile. Method: This was a retrospective study in a secondary level hospital from the period of 2014–2020. The patients’ demographic data, clinical features, location of infection, comorbidities, laboratory and microbiological profiles were analysed. Results: There were 53 patients during 2014–2020 with median age of 45.5 (38.5–56.0) years. The majority of the patients were males (35 [66.04%]), had no comorbidities (25 [47.17%]), and the lower limb was the most common anatomic site (17 [32.08%]). Type II (monomicrobial) NF was the predominant type (31 [58.49%]). Staphylococcus aureus was the most prevalent Gram-positive bacteria (18 [38%]) and Escherichia coli, the main species isolated in the Gram-negative bacteria (14 [36%]) with susceptibility to cloxacillin (94%) and amoxicillin and/or clavulanic acid (92%), respectively. Conclusion: Staphylococcus aureus and Escherichia coli were the most common bacteria with low rate of antimicrobial resistance. Amoxicillin and/or clavulanic acid and an adjunctive clindamycin are appropriate antimicrobial therapy for empiric treatment for NF in our setting. Contribution: Amoxicillin and/or clavulanic acid and an adjunctive clindamycin can be used as an empiric treatment for NF

Optimizing sparse RFI prediction using deep learning

Radio frequency interference (RFI) is an ever-present limiting factor among radio telescopes even in the most remote observing locations. When looking to retain the maximum amount of sensitivity and reduce contamination for Epoch of Reionization studies, the identification and removal of RFI is especially important. In addition to improved RFI identification, we must also take into account computational efficiency of the RFI-Identification algorithm as radio interferometer arrays such as the Hydrogen Epoch of Reionization Array (HERA) grow larger in number of receivers. To address this, we present a deep fully convolutional neural network (DFCN) that is comprehensive in its use of interferometric data, where both amplitude and phase information are used jointly for identifying RFI. We train the network using simulated HERA visibilities containing mock RFI, yielding a known \u2018ground truth\u2019 data set for evaluating the accuracy of various RFI algorithms. Evaluation of the DFCN model is performed on observations from the 67 dish build-out, HERA-67, and achieves a data throughput of 1.6 7 105 HERA time-ordered 1024 channelled visibilities per hour per GPU. We determine that relative to an amplitude only network including visibility phase adds important adjacent time\u2013frequency context which increases discrimination between RFI and non-RFI. The inclusion of phase when predicting achieves a recall of 0.81, precision of 0.58, and F2 score of 0.75 as applied to our HERA-67 observations

Measuring HERA's Primary Beam in Situ: Methodology and First Results

The central challenge in 21 cm cosmology is isolating the cosmological signal from bright foregrounds. Many separation techniques rely on the accurate knowledge of the sky and the instrumental response, including the antenna primary beam. For drift-scan telescopes, such as the Hydrogen Epoch of Reionization Array (HERA), that do not move, primary beam characterization is particularly challenging because standard beam-calibration routines do not apply (Cornwell et al.) and current techniques require accurate source catalogs at the telescope resolution. We present an extension of the method from Pober et al. where they use beam symmetries to create a network of overlapping source tracks that break the degeneracy between source flux density and beam response and allow their simultaneous estimation. We fit the beam response of our instrument using early HERA observations and find that our results agree well with electromagnetic simulations down to a -20 dB level in power relative to peak gain for sources with high signal-to-noise ratio. In addition, we construct a source catalog with 90 sources down to a flux density of 1.4 Jy at 151 MHz.The central challenge in 21 cm cosmology is isolating the cosmological signal from bright foregrounds. Many separation techniques rely on the accurate knowledge of the sky and the instrumental response, including the antenna primary beam. For drift-scan telescopes, such as the Hydrogen Epoch of Reionization Array (HERA), that do not move, primary beam characterization is particularly challenging because standard beam-calibration routines do not apply (Cornwell et al.) and current techniques require accurate source catalogs at the telescope resolution. We present an extension of the method from Pober et al. where they use beam symmetries to create a network of overlapping source tracks that break the degeneracy between source flux density and beam response and allow their simultaneous estimation. We fit the beam response of our instrument using early HERA observations and find that our results agree well with electromagnetic simulations down to a -20 dB level in power relative to peak gain for sources with high signal-to-noise ratio. In addition, we construct a source catalog with 90 sources down to a flux density of 1.4 Jy at 151 MHz

A Real Time Processing system for big data in astronomy: Applications to HERA

As current- and next-generation astronomical instruments come online, they will generate an unprecedented deluge of data. Analyzing these data in real time presents unique conceptual and computational challenges, and their long-term storage and archiving is scientifically essential for generating reliable, reproducible results. We present here the real-time processing (RTP) system for the Hydrogen Epoch of Reionization Array (HERA), a radio interferometer endeavoring to provide the first detection of the highly redshifted 21 cm signal from Cosmic Dawn and the Epoch of Reionization by an interferometer. The RTP system consists of analysis routines run on raw data shortly after they are acquired, such as calibration and detection of radio-frequency interference (RFI) events. RTP works closely with the Librarian, the HERA data storage and transfer manager which automatically ingests data and transfers copies to other clusters for post-processing analysis. Both the RTP system and the Librarian are public and open source software, which allows for them to be modified for use in other scientific collaborations. When fully constructed, HERA is projected to generate over 50 terabytes (TB) of data each night, and the RTP system enables the successful scientific analysis of these data

Detection of cosmic structures using the bispectrum phase. II. First results from application to cosmic reionization using the Hydrogen Epoch of Reionization Array

Characterizing the epoch of reionization (EoR) at $z\gtrsim 6$ via the redshifted 21 cm line of neutral Hydrogen (HI) is critical to modern astrophysics and cosmology, and thus a key science goal of many current and planned low-frequency radio telescopes. The primary challenge to detecting this signal is the overwhelmingly bright foreground emission at these frequencies, placing stringent requirements on the knowledge of the instruments and inaccuracies in analyses. Results from these experiments have largely been limited not by thermal sensitivity but by systematics, particularly caused by the inability to calibrate the instrument to high accuracy. The interferometric bispectrum phase is immune to antenna-based calibration and errors therein, and presents an independent alternative to detect the EoR HI fluctuations while largely avoiding calibration systematics. Here, we provide a demonstration of this technique on a subset of data from the Hydrogen Epoch of Reionization Array (HERA) to place approximate constraints on the IGM brightness temperature. From this limited data, at $z=7.7$ we infer "$1\sigma$" upper limits on the IGM brightness temperature to be $\le 316$ "pseudo" mK at $\kappa_\parallel=0.33\,\textrm{"pseudo"}\,h$ Mpc$^{-1}$ (data-limited) and $\le 1000$ "pseudo" mK at $\kappa_\parallel=0.875\,\textrm{"pseudo"}\,h$ Mpc$^{-1}$ (noise-limited). The "pseudo" units denote only an approximate and not an exact correspondence to the actual distance scales and brightness temperatures. By propagating models in parallel to the data analysis, we confirm that the dynamic range required to separate the cosmic HI signal from the foregrounds is similar to that in standard approaches, and the power spectrum of the bispectrum phase is still data-limited (at $\gtrsim 10^6$ dynamic range) indicating scope for further improvement in sensitivity as the array build-out continues

Detection of cosmic structures using the bispectrum phase. II. First results from application to cosmic reionization using the Hydrogen Epoch of Reionization Array

Characterizing the epoch of reionization (EoR) at $z\gtrsim 6$ via the redshifted 21 cm line of neutral Hydrogen (HI) is critical to modern astrophysics and cosmology, and thus a key science goal of many current and planned low-frequency radio telescopes. The primary challenge to detecting this signal is the overwhelmingly bright foreground emission at these frequencies, placing stringent requirements on the knowledge of the instruments and inaccuracies in analyses. Results from these experiments have largely been limited not by thermal sensitivity but by systematics, particularly caused by the inability to calibrate the instrument to high accuracy. The interferometric bispectrum phase is immune to antenna-based calibration and errors therein, and presents an independent alternative to detect the EoR HI fluctuations while largely avoiding calibration systematics. Here, we provide a demonstration of this technique on a subset of data from the Hydrogen Epoch of Reionization Array (HERA) to place approximate constraints on the IGM brightness temperature. From this limited data, at $z=7.7$ we infer "$1\sigma$" upper limits on the IGM brightness temperature to be $\le 316$ "pseudo" mK at $\kappa_\parallel=0.33\,\textrm{"pseudo"}\,h$ Mpc$^{-1}$ (data-limited) and $\le 1000$ "pseudo" mK at $\kappa_\parallel=0.875\,\textrm{"pseudo"}\,h$ Mpc$^{-1}$ (noise-limited). The "pseudo" units denote only an approximate and not an exact correspondence to the actual distance scales and brightness temperatures. By propagating models in parallel to the data analysis, we confirm that the dynamic range required to separate the cosmic HI signal from the foregrounds is similar to that in standard approaches, and the power spectrum of the bispectrum phase is still data-limited (at $\gtrsim 10^6$ dynamic range) indicating scope for further improvement in sensitivity as the array build-out continues

Imaging and Modeling Data from the Hydrogen Epoch of Reionization Array

We analyze data from the Hydrogen Epoch of Reionization Array. This is the third in a series of papers on the closure phase delay-spectrum technique designed to detect the HI 21cm emission from cosmic reionization. We present the details of the data and models employed in the power spectral analysis, and discuss limitations to the process. We compare images and visibility spectra made with HERA data, to parallel quantities generated from sky models based on the GLEAM survey, incorporating the HERA telescope model. We find reasonable agreement between images made from HERA data, with those generated from the models, down to the confusion level. For the visibility spectra, there is broad agreement between model and data across the full band of $\sim 80$MHz. However, models with only GLEAM sources do not reproduce a roughly sinusoidal spectral structure at the tens of percent level seen in the observed visibility spectra on scales $\sim 10$ MHz on 29 m baselines. We find that this structure is likely due to diffuse Galactic emission, predominantly the Galactic plane, filling the far sidelobes of the antenna primary beam. We show that our current knowledge of the frequency dependence of the diffuse sky radio emission, and the primary beam at large zenith angles, is inadequate to provide an accurate reproduction of the diffuse structure in the models. We discuss implications due to this missing structure in the models, including calibration, and in the search for the HI 21cm signal, as well as possible mitigation techniques

Understanding the HERA Phase i receiver system with simulations and its impact on the detectability of the EoR delay power spectrum

The detection of the Epoch of Reionization (EoR) delay power spectrum using a "foreground avoidance method" highly depends on the instrument chromaticity. The systematic effects induced by the radio-telescope spread the foreground signal in the delay domain, which contaminates the EoR window theoretically observable. Applied to the Hydrogen Epoch of Reionization Array (HERA), this paper combines detailed electromagnetic and electrical simulations in order to model the chromatic effects of the instrument, and quantify its frequency and time responses. In particular, the effects of the analogue receiver, transmission cables, and mutual coupling are included. These simulations are able to accurately predict the intensity of the reflections occurring in the 150-m cable which links the antenna to the back-end. They also show that electromagnetic waves can propagate from one dish to another one through large sections of the array due to mutual coupling. The simulated system time response is attenuated by a factor $10^{4}$ after a characteristic delay which depends on the size of the array and on the antenna position. Ultimately, the system response is attenuated by a factor $10^{5}$ after 1400 ns because of the reflections in the cable, which corresponds to characterizable ${k_\parallel}$-modes above 0.7 $h\;\rm{Mpc}^{-1}$ at 150 MHz. Thus, this new study shows that the detection of the EoR signal with HERA Phase I will be more challenging than expected. On the other hand, it improves our understanding of the telescope, which is essential to mitigate the instrument chromaticity

Automated Detection of Antenna Malfunctions in Large-N Interferometers: A case study With the Hydrogen Epoch of Reionization Array

We present a framework for identifying and flagging malfunctioning antennas in large radio interferometers. We outline two distinct categories of metrics designed to detect outliers along known failure modes of large arrays: cross-correlation metrics, based on all antenna pairs, and auto-correlation metrics, based solely on individual antennas. We define and motivate the statistical framework for all metrics used, and present tailored visualizations that aid us in clearly identifying new and existing systematics. We implement these techniques using data from 105 antennas in the Hydrogen Epoch of Reionization Array (HERA) as a case study. Finally, we provide a detailed algorithm for implementing these metrics as flagging tools on real data sets