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1. A demonstration of the effect of fringe-rate filtering in the Hydrogen Epoch of Reionization Array delay power spectrum pipeline

Author

Garsden, Hugh, Bull, Philip, Wilensky, Mike, Abdurashidova, Zuhra, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Berkhout, Lindsay M., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Burba, Jacob, Carey, Steven, Carilli, Chris L., Chen, Kai-Feng, Cheng, Carina, Choudhuri, Samir, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Dillon, Joshua S., Dynes, Scott, Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Gehlot, Bharat Kumar, Ghosh, Abhik, Glendenning, Brian, Gorce, Adelie, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hazelton, Bryna J., Hewitt, Jacqueline N., Hickish, Jack, Huang, Tian, Jacobs, Daniel C., Josaitis, Alec, Julius, Austin, Kariseb, MacCalvin, Kern, Nicholas S., Kerrigan, Joshua, Kim, Honggeun, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Liu, Adrian, Loots, Anita, Ma, Yin-Zhe, MacMahon, David H. E., Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Morales, Miguel F., Mosiane, Tshegofalang, Murray, Steven G., Neben, Abraham R., Nikolic, Bojan, Nunhokee, Chuneeta Devi, Nuwegeld, Hans, Parsons, Aaron R., Pascua, Robert, Patra, Nipanjana, Pieterse, Samantha, Qin, Yuxiang, Rath, Eleanor, Razavi-Ghods, Nima, Riley, Daniel, Robnett, James, Rosie, Kathryn, Santos, Mario G., Sims, Peter, Singh, Saurabh, Storer, Dara, Swarts, Hilton, Tan, Jianrong, Thyagarajan, Nithyanandan, van Wyngaarden, Pieter, Williams, Peter K. G., Xu, Zhilei, and Zheng, Haoxuan

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Radio interferometers targeting the 21cm brightness temperature fluctuations at high redshift are subject to systematic effects that operate over a range of different timescales. These can be isolated by designing appropriate Fourier filters that operate in fringe-rate (FR) space, the Fourier pair of local sidereal time (LST). Applications of FR filtering include separating effects that are correlated with the rotating sky vs. those relative to the ground, down-weighting emission in the primary beam sidelobes, and suppressing noise. FR filtering causes the noise contributions to the visibility data to become correlated in time however, making interpretation of subsequent averaging and error estimation steps more subtle. In this paper, we describe fringe rate filters that are implemented using discrete prolate spheroidal sequences, and designed for two different purposes -- beam sidelobe/horizon suppression (the `mainlobe' filter), and ground-locked systematics removal (the `notch' filter). We apply these to simulated data, and study how their properties affect visibilities and power spectra generated from the simulations. Included is an introduction to fringe-rate filtering and a demonstration of fringe-rate filters applied to simple situations to aid understanding., Comment: 21 pages, 18 figures, submitted to Monthly Notices of the Royal Astronomical Society

Published
2024

2. Hydrogen Epoch of Reionization Array (HERA) Phase II Deployment and Commissioning

Author

Berkhout, Lindsay M., Jacobs, Daniel C., Abdurashidova, Zuhra, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Bull, Philip, Burba, Jacob, Carey, Steven, Carilli, Chris L., Chen, Kai-Feng, Cheng, Carina, Choudhuri, Samir, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Dillon, Joshua S., Dynes, Scott, Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Garsden, Hugh, Gehlot, Bharat Kumar, Ghosh, Abhik, Glendenning, Brian, Gorce, Adelie, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hazelton, Bryna J., Hewitt, Jacqueline N., Hickish, Jack, Huang, Tian, Josaitis, Alec, Julius, Austin, Kariseb, MacCalvin, Kern, Nicholas S., Kerrigan, Joshua, Kim, Honggeun, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Liu, Adrian, Loots, Anita, Ma, Yin-Zhe, MacMahon, David Harold Edward, Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Morales, Miguel F., Mosiane, Tshegofalang, Murray, Steven G., Neben, Abraham R., Nikolic, Bojan, Nunhokee, Chuneeta Devi, Nuwegeld, Hans, Parsons, Aaron R., Pascua, Robert, Patra, Nipanjana, Pieterse, Samantha, Qin, Yuxiang, Rath, Eleanor, Razavi-Ghods, Nima, Riley, Daniel, Robnett, James, Rosie, Kathryn, Santos, Mario G., Sims, Peter, Singh, Saurabh, Storer, Dara, Swarts, Hilton, Tan, Jianrong, Thyagarajan, Nithyanandan, van Wyngaarden, Pieter, Williams, Peter K. G., Zheng, Haoxuan, and Xu, Zhilei

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

This paper presents the design and deployment of the Hydrogen Epoch of Reionization Array (HERA) phase II system. HERA is designed as a staged experiment targeting 21 cm emission measurements of the Epoch of Reionization. First results from the phase I array are published as of early 2022, and deployment of the phase II system is nearing completion. We describe the design of the phase II system and discuss progress on commissioning and future upgrades. As HERA is a designated Square Kilometer Array (SKA) pathfinder instrument, we also show a number of "case studies" that investigate systematics seen while commissioning the phase II system, which may be of use in the design and operation of future arrays. Common pathologies are likely to manifest in similar ways across instruments, and many of these sources of contamination can be mitigated once the source is identified.

Published
2024
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3. matvis: A matrix-based visibility simulator for fast forward modelling of many-element 21 cm arrays

Author

Kittiwisit, Piyanat, Murray, Steven G., Garsden, Hugh, Bull, Philip, Cain, Christopher, Parsons, Aaron R., Sipple, Jackson, Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Berkhout, Lindsay M., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Burba, Jacob, Carey, Steven, Carilli, Chris L., Chen, Kai-Feng, Cheng, Carina, Choudhuri, Samir, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Dillon, Joshua S., Dynes, Scott, Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Gehlot, Bharat Kumar, Ghosh, Abhik, Glendenning, Brian, Gorce, Adelie, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hazelton, Bryna J., Hewitt, Jacqueline N., Hickish, Jack, Huang, Tian, Jacobs, Daniel C., Josaitis, Alec, Julius, Austin, Kariseb, MacCalvin, Kern, Nicholas S., Kerrigan, Joshua, Kim, Honggeun, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Liu, Adrian, Loots, Anita, Ma, Yin-Zhe, MacMahon, David H. E., Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Morales, Miguel F., Mosiane, Tshegofalang, Neben, Abraham R., Nikolic, Bojan, Nunhokee, Chuneeta Devi, Nuwegeld, Hans, Pascua, Robert, Patra, Nipanjana, Pieterse, Samantha, Qin, Yuxiang, Rath, Eleanor, Razavi-Ghods, Nima, Riley, Daniel, Robnett, James, Rosie, Kathryn, Santos, Mario G., Sims, Peter, Singh, Saurabh, Storer, Dara, Swarts, Hilton, Tan, Jianrong, Thyagarajan, Nithyanandan, van Wyngaarden, Pieter, Williams, Peter K. G., Xu, Zhilei, and Zheng, Haoxuan

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Detection of the faint 21 cm line emission from the Cosmic Dawn and Epoch of Reionisation will require not only exquisite control over instrumental calibration and systematics to achieve the necessary dynamic range of observations but also validation of analysis techniques to demonstrate their statistical properties and signal loss characteristics. A key ingredient in achieving this is the ability to perform high-fidelity simulations of the kinds of data that are produced by the large, many-element, radio interferometric arrays that have been purpose-built for these studies. The large scale of these arrays presents a computational challenge, as one must simulate a detailed sky and instrumental model across many hundreds of frequency channels, thousands of time samples, and tens of thousands of baselines for arrays with hundreds of antennas. In this paper, we present a fast matrix-based method for simulating radio interferometric measurements (visibilities) at the necessary scale. We achieve this through judicious use of primary beam interpolation, fast approximations for coordinate transforms, and a vectorised outer product to expand per-antenna quantities to per-baseline visibilities, coupled with standard parallelisation techniques. We validate the results of this method, implemented in the publicly-available matvis code, against a high-precision reference simulator, and explore its computational scaling on a variety of problems., Comment: 25 pages, 20 figures, submitted to RAS Techniques and Instruments, matvis is publicly available at https://github.com/HERA-Team/matvis

Published
2023

4. Bayesian estimation of cross-coupling and reflection systematics in 21cm array visibility data

Author

Murphy, Geoff G., Bull, Philip, Santos, Mario G., Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Bernardi, Gianni, Billings, Tashalee, Bowman, Judd D., Bradley, Richard F., Burba, Jacob, Cain, Christopher, Carey, Steven, Carilli, Chris L., Cheng, Carina, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Dillon, Joshua S., Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Glendenning, Brian, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hazelton, Bryna J., Hewitt, Jacqueline N., Hickish, Jack, Jacobs, Daniel C., Julius, Austin, Kariseb, MacCalvin, Kern, Nicholas S., Kerrigan, Joshua, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Liu, Adrian, Loots, Anita, MacMahon, David Harold Edward, Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Morales, Miguel F., Mosiane, Tshegofalang, Murray, Steven G., Neben, Abraham R., Nikolic, Bojan, Nuwegeld, Hans, Parsons, Aaron R., Patra, Nipanjana, Pieterse, Samantha, Razavi-Ghods, Nima, Robnett, James, Rosie, Kathryn, Sims, Peter, Sipple, Jackson, Smith, Craig, Swarts, Hilton, Thyagarajan, Nithyanandan, van Wyngaarden, Pieter, Williams, Peter K. G., and Zheng, Haoxuan

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

Observations with radio arrays that target the 21-cm signal originating from the early Universe suffer from a variety of systematic effects. An important class of these are reflections and spurious couplings between antennas. We apply a Hamiltonian Monte Carlo sampler to the modelling and mitigation of these systematics in simulated Hydrogen Epoch of Reionisation Array (HERA) data. This method allows us to form statistical uncertainty estimates for both our models and the recovered visibilities, which is an important ingredient in establishing robust upper limits on the Epoch of Reionisation (EoR) power spectrum. In cases where the noise is large compared to the EoR signal, this approach can constrain the systematics well enough to mitigate them down to the noise level for both systematics studied. Where the noise is smaller than the EoR, our modelling can mitigate the majority of the reflections with there being only a minor level of residual systematics, while cross-coupling sees essentially complete mitigation. Our approach performs similarly to existing filtering/fitting techniques used in the HERA pipeline, but with the added benefit of rigorously propagating uncertainties. In all cases it does not significantly attenuate the underlying signal., Comment: 19 pages, 14 figures, submitted to MNRAS

Published
2023

5. A germ-free humanized mouse model shows the contribution of resident microbiota to human-specific pathogen infection

Author

Wahl, Angela, Yao, Wenbo, Liao, Baolin, Chateau, Morgan, Richardson, Cara, Ling, Lijun, Franks, Adrienne, Senthil, Krithika, Doyon, Genevieve, Li, Fengling, Frost, Josh, Whitehurst, Christopher B., Pagano, Joseph S., Fletcher, Craig A., Azcarate-Peril, M. Andrea, Hudgens, Michael G., Rogala, Allison R., Tucker, Joseph D., McGowan, Ian, Sartor, R. Balfour, and Garcia, J. Victor

Published
2024
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6. Direct Optimal Mapping Image Power Spectrum and its Window Functions

Author

Xu, Zhilei, Kim, Honggeun, Hewitt, Jacqueline N., Chen, Kai-Feng, Kern, Nicholas S., Rath, Eleanor, Byrne, Ruby, Gorce, Adélie, Pascua, Robert, Martinot, Zachary E., Dillon, Joshua S., Hazelton, Bryna J., Liu, Adrian, Morales, Miguel F., Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Bull, Philip, Burba, Jacob, Carey, Steven, Carilli, Chris L., Cheng, Carina, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Glendenning, Brian, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hickish, Jack, Jacobs, Daniel C., Julius, Austin, Kariseb, MacCalvin, Kerrigan, Joshua, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Loots, Anita, MacMahon, David Harold Edward, Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Mesinger, Andrei, Molewa, Mathakane, Mosiane, Tshegofalang, Murray, Steven G., Neben, Abraham R., Nikolic, Bojan, Nuwegeld, Hans, Parsons, Aaron R., Patra, Nipanjana, Pieterse, Samantha, Razavi-Ghods, Nima, Robnett, James, Rosie, Kathryn, Sims, Peter, Smith, Craig, Swarts, Hilton, Thyagarajan, Nithyanandan, van Wyngaarden, Pieter, Williams, Peter K. G., and Zheng, Haoxuan

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

The key to detecting neutral hydrogen during the epoch of reionization (EoR) is to separate the cosmological signal from the dominating foreground radiation. We developed direct optimal mapping (DOM) to map interferometric visibilities; it contains only linear operations, with full knowledge of point spread functions from visibilities to images. Here, we demonstrate a fast Fourier transform-based image power spectrum and its window functions computed from the DOM images. We use noiseless simulation, based on the Hydrogen Epoch of Reionization Array Phase I configuration, to study the image power spectrum properties. The window functions show $<10^{-11}$ of the integrated power leaks from the foreground-dominated region into the EoR window; the 2D and 1D power spectra also verify the separation between the foregrounds and the EoR., Comment: Published in ApJ

Published
2023

7. Patient Flow and Reutilization of Crisis Services Within 30 Days in a Comprehensive Crisis System.

Author

Tomovic, Milos, Balfour, Margaret E, Cho, Ted, Prathap, Nishanth, Harootunian, Gevork, Mehreen, Raihana, Ostrovsky, Andrey, and Goldman, Matthew L

Subjects
Health Services and Systems, Health Sciences, Clinical Research, Health Services, Community mental health services, Crisis intervention, Crisis stabilization, Involuntary commitment, Psychiatric emergency services, Services utilization, Public Health and Health Services, Psychiatry, Clinical sciences, Health services and systems
Abstract

ObjectiveCrisis services are undergoing an unprecedented expansion in the United States, but research is lacking on crisis system design. This study describes how individuals flow through a well-established crisis system and examines factors associated with reutilization of such services.MethodsThis cross-sectional study used Medicaid claims to construct episodes describing the flow of individuals through mobile crisis, specialized crisis facility, emergency department, and inpatient services. Claims data were merged with electronic health record (EHR) data for the subset of individuals receiving care at a crisis response center. A generalized estimating equation was used to calculate adjusted odds ratios for demographic, clinical, and operational factors associated with reutilization of services within 30 days of an episode's end point.ResultsOf 41,026 episodes, most (57.4%) began with mobile crisis services or a specialized crisis facility rather than the emergency department. Of the subset (N=9,202 episodes) with merged EHR data, most episodes (63.3%) were not followed by reutilization. Factors associated with increased odds of 30-day reutilization included Black race, homelessness, stimulant use, psychosis, and episodes beginning with mobile crisis services or ending with inpatient care. Decreased odds were associated with depression, trauma, and involuntary legal status. Most (59.3%) episodes beginning with an involuntary legal status ended with a voluntary status.ConclusionsCrisis systems can serve a large proportion of individuals experiencing psychiatric emergencies and divert them from more restrictive and costly levels of care. Understanding demographic, clinical, and operational factors associated with 30-day reutilization may aid in the design and implementation of crisis systems.

Published
2024

10. Mouse adaptation of human inflammatory bowel diseases microbiota enhances colonization efficiency and alters microbiome aggressiveness depending on the recipient colonic inflammatory environment

Author

Simon M. Gray, Anh D. Moss, Jeremy W. Herzog, Saori Kashiwagi, Bo Liu, Jacqueline B. Young, Shan Sun, Aadra P. Bhatt, Anthony A. Fodor, and R. Balfour Sartor

Subjects
Inflammatory bowel diseases, Experimental colitis, Human microbiota associated mice, Fecal microbiota transplant, Microbiota transfer efficiency, Mouse-adapted, Microbial ecology, QR100-130
Abstract

Abstract Background Understanding the cause vs consequence relationship of gut inflammation and microbial dysbiosis in inflammatory bowel diseases (IBD) requires a reproducible mouse model of human-microbiota-driven experimental colitis. Results Our study demonstrated that human fecal microbiota transplant (FMT) transfer efficiency is an underappreciated source of experimental variability in human microbiota-associated (HMA) mice. Pooled human IBD patient fecal microbiota engrafted germ-free (GF) mice with low amplicon sequence variant (ASV)-level transfer efficiency, resulting in high recipient-to-recipient variation of microbiota composition and colitis severity in HMA Il-10 −/− mice. In contrast, mouse-to-mouse transfer of mouse-adapted human IBD patient microbiota transferred with high efficiency and low compositional variability resulting in highly consistent and reproducible colitis phenotypes in recipient Il-10 −/− mice. Engraftment of human-to-mouse FMT stochastically varied with individual transplantation events more than mouse-adapted FMT. Human-to-mouse FMT caused a population bottleneck with reassembly of microbiota composition that was host inflammatory environment specific. Mouse-adaptation in the inflamed Il-10 −/− host reassembled a more aggressive microbiota that induced more severe colitis in serial transplant to Il-10 −/− mice than the distinct microbiota reassembled in non-inflamed WT hosts. Conclusions Our findings support a model of IBD pathogenesis in which host inflammation promotes aggressive resident bacteria, which further drives a feed-forward process of dysbiosis exacerbated by gut inflammation. This model implies that effective management of IBD requires treating both the dysregulated host immune response and aggressive inflammation-driven microbiota. We propose that our mouse-adapted human microbiota model is an optimized, reproducible, and rigorous system to study human microbiome-driven disease phenotypes, which may be generalized to mouse models of other human microbiota-modulated diseases, including metabolic syndrome/obesity, diabetes, autoimmune diseases, and cancer. Video Abstract

Published
2024
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11. Risky conclusions regarding shrinking rhino horns

Author

S. M. Ferreira, M. ’t Sas‐Rolfes, D. Balfour, C. Barichievy, G. Chege, C. Dean, N. Doak, H. T. Dublin, R. duToit, S. Ellis, R. H. Emslie, J. Flamand, M. Gadd, J. Gaymer, M. Hofmeyr, M. Knight, Y. Moodley, J. Shaw, L. Versteege, L. Vigne, F. vonHouwald, S. Uri‐Khob, and K. Mosweu

Subjects
poaching, rhino horn, trophy hunting, Human ecology. Anthropogeography, GF1-900, Ecology, QH540-549.5
Abstract

Abstract Image‐based analyses from an online repository on rhino horns asserted that declines in size over time could be the consequence of poaching and hunting. We provide reflections on whether the sample was representative enough to make generalizations, the study adequately accounted for the main sources of horn‐size variation and the statistical methods were adequate to be confident in the results. The sample had a limited representation, most coming from zoo animals. We highlight several sources of variance in horn size that such a sample could not evaluate robustly using linear regressions, both for establishing a proxy for horn size corrected for size of a rhino and assessing trends over time. Nevertheless, horn poaching continues to be the key threat to rhinos. Addressing the underlying drivers of poaching and trafficking are key priorities for responsible public debate, policy making and interventions. Read the free Plain Language Summary for this article on the Journal blog.

Published
2024
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12. Consensus Guidelines for Perioperative Care for Emergency Laparotomy Enhanced Recovery After Surgery (ERAS®) Society Recommendations Part 2-Emergency Laparotomy: Intra- and Postoperative Care.

Author

Scott, Michael, Aggarwal, Geeta, Aitken, Robert, Anderson, Iain, Balfour, Angie, Foss, Nicolai, Cooper, Zara, Dhesi, Jugdeep, French, W, Grant, Michael, Hammarqvist, Folke, Hare, Sarah, Havens, Joaquim, Holena, Daniel, Hübner, Martin, Johnston, Carolyn, Kim, Jeniffer, Lees, Nicholas, Ljungqvist, Olle, Lobo, Dileep, Mohseni, Shahin, Ordoñez, Carlos, Quiney, Nial, Sharoky, Catherine, Urman, Richard, Wu, Christopher, Young-Fadok, Tonia, Peden, Carol, and Wick, Elizabeth

Subjects
Humans, Enhanced Recovery After Surgery, Postoperative Care, Laparotomy, Perioperative Care, Elective Surgical Procedures
Abstract

BACKGROUND: This is Part 2 of the first consensus guidelines for optimal care of patients undergoing emergency laparotomy (EL) using an Enhanced Recovery After Surgery (ERAS) approach. This paper addresses intra- and postoperative aspects of care. METHODS: Experts in aspects of management of high-risk and emergency general surgical patients were invited to contribute by the International ERAS® Society. PubMed, Cochrane, Embase, and Medline database searches were performed for ERAS elements and relevant specific topics. Studies on each item were selected with particular attention to randomized clinical trials, systematic reviews, meta-analyses, and large cohort studies and reviewed and graded using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) system. Recommendations were made on the best level of evidence, or extrapolation from studies on elective patients when appropriate. A modified Delphi method was used to validate final recommendations. Some ERAS® components covered in other guideline papers are outlined only briefly, with the bulk of the text focusing on key areas pertaining specifically to EL. RESULTS: Twenty-three components of intraoperative and postoperative care were defined. Consensus was reached after three rounds of a modified Delphi Process. CONCLUSIONS: These guidelines are based on best available evidence for an ERAS® approach to patients undergoing EL. These guidelines are not exhaustive but pull together evidence on important components of care for this high-risk patient population. As much of the evidence is extrapolated from elective surgery or emergency general surgery (not specifically laparotomy), many of the components need further evaluation in future studies.

Published
2023

13. Enhanced Recovery After Surgery (ERAS®) Society Consensus Guidelines for Emergency Laparotomy Part 3: Organizational Aspects and General Considerations for Management of the Emergency Laparotomy Patient.

Author

Peden, Carol, Aggarwal, Geeta, Aitken, Robert, Anderson, Iain, Balfour, Angie, Foss, Nicolai, Cooper, Zara, Dhesi, Jugdeep, French, W, Grant, Michael, Hammarqvist, Folke, Hare, Sarah, Havens, Joaquim, Holena, Daniel, Hübner, Martin, Johnston, Carolyn, Kim, Jeniffer, Lees, Nicholas, Ljungqvist, Olle, Lobo, Dileep, Mohseni, Shahin, Ordoñez, Carlos, Quiney, Nial, Sharoky, Catherine, Urman, Richard, Wu, Christopher, Young-Fadok, Tonia, Scott, Michael, and Wick, Elizabeth

Subjects
Humans, Enhanced Recovery After Surgery, Laparotomy, Perioperative Care, Organizations, Elective Surgical Procedures
Abstract

BACKGROUND: This is Part 3 of the first consensus guidelines for optimal care of patients undergoing emergency laparotomy using an enhanced recovery after surgery (ERAS) approach. This paper addresses organizational aspects of care. METHODS: Experts in management of the high-risk and emergency general surgical patient were invited to contribute by the International ERAS® Society. PubMed, Cochrane, Embase, and MEDLINE database searches were performed for ERAS elements and relevant specific topics. Studies were selected with particular attention to randomized clinical trials, systematic reviews, meta-analyses and large cohort studies, and reviewed and graded using the Grading of Recommendations, Assessment, Development and Evaluation system. Recommendations were made on the best level of evidence, or extrapolation from studies on elective patients when appropriate. A modified Delphi method was used to validate final recommendations. RESULTS: Components of organizational aspects of care were considered. Consensus was reached after three rounds of a modified Delphi process. CONCLUSIONS: These guidelines are based on best current available evidence for organizational aspects of an ERAS® approach to patients undergoing emergency laparotomy and include discussion of less common aspects of care for the surgical patient, including end-of-life issues. These guidelines are not exhaustive but pull together evidence on important components of care for this high-risk patient population. As much of the evidence is extrapolated from elective surgery or emergency general surgery (not specifically laparotomy), many of the components need further evaluation in future studies.

Published
2023

14. Search for the Epoch of Reionisation with HERA: Upper Limits on the Closure Phase Delay Power Spectrum

Author

Keller, Pascal M., Nikolic, Bojan, Thyagarajan, Nithyanandan, Carilli, Chris L., Bernardi, Gianni, Charles, Ntsikelelo, Bester, Landman, Smirnov, Oleg M., Kern, Nicholas S., Dillon, Joshua S., Hazelton, Bryna J., Morales, Miguel F., Jacobs, Daniel C., Parsons, Aaron R., Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Bull, Philip, Burba, Jacob, Carey, Steven, Cheng, Carina, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Glendenning, Brian, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hewitt, Jacqueline N., Hickish, Jack, Julius, Austin, Kariseb, MacCalvin, Kerrigan, Joshua, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Liu, Adrian, Loots, Anita, Ma, Yin-Zhe, MacMahon, David Harold Edward, Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Mosiane, Tshegofalang, Murray, Steven G., Neben, Abraham R., Nuwegeld, Hans, Pascua, Robert, Patra, Nipanjana, Pieterse, Samantha, Pober, Jonathan C., Razavi-Ghods, Nima, Robnett, James, Rosie, Kathryn, Santos, Mario G., Sims, Peter, Smith, Craig, Swarts, Hilton, Van Wyngaarden, Pieter, Williams, Peter K. G., and Zheng, Haoxuan

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Radio interferometers aiming to measure the power spectrum of the redshifted 21 cm line during the Epoch of Reionisation (EoR) need to achieve an unprecedented dynamic range to separate the weak signal from overwhelming foreground emissions. Calibration inaccuracies can compromise the sensitivity of these measurements to the effect that a detection of the EoR is precluded. An alternative to standard analysis techniques makes use of the closure phase, which allows one to bypass antenna-based direction-independent calibration. Similarly to standard approaches, we use a delay spectrum technique to search for the EoR signal. Using 94 nights of data observed with Phase I of the Hydrogen Epoch of Reionization Array (HERA), we place approximate constraints on the 21 cm power spectrum at $z=7.7$. We find at 95% confidence that the 21 cm EoR brightness temperature is $\le$(372)$^2$ "pseudo" mK$^2$ at 1.14 "pseudo" $h$ Mpc$^{-1}$, where the "pseudo" emphasises that these limits are to be interpreted as approximations to the actual distance scales and brightness temperatures. Using a fiducial EoR model, we demonstrate the feasibility of detecting the EoR with the full array. Compared to standard methods, the closure phase processing is relatively simple, thereby providing an important independent check on results derived using visibility intensities, or related., Comment: 16 pages, 14 figures, accepted for publication by MNRAS

Published
2023
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15. Post‐Copulatory Sexual Selection in an Insect With High Levels of Mating Failure

Author

Vicki L. Balfour, Mélissa Armand, and David M. Shuker

Subjects
cryptic male choice, Lygaeus simulans, mate choice, mating failure, post‐copulatory sexual selection, sperm competition, Ecology, QH540-549.5
Abstract

ABSTRACT Sexual selection is not a single process. Instead, multiple processes of sexual selection can interact with respect to a given phenotype, in either reinforcing, independent, or conflicting directions. Here we consider how different processes of sexual selection interact in the seed bug Lygaeus simulans. This species is characterised by limited pre‐copulatory sexual selection, but the potential for rather strong post‐copulatory sexual selection. In particular, mating failure is common in this species, with around 40%–60% of copulations failing to result in the successful transfer of sperm. Mating failure is negatively correlated with female size, with smaller females being less likely to end up inseminated. We have recently argued that this pattern is best explained by cryptic male mate choice for large, more fecund females. Males therefore preferentially inseminate larger females. Here we explore how this potential cryptic male choice interacts with another component of post‐copulatory sexual selection: sperm competition. We first manipulated male and female size variation, generating large and small, male and female, size classes. Using a visible mutant marker to assign paternity, we then double‐mated females with males, in all combinations of male and female size. Our results showed that sperm competition outcomes were primarily driven by copulation duration, with longer copulations leading to greater paternity share for a male. We also confirmed that larger females are more likely to produce offspring than smaller females, as predicted by cryptic male choice for large females. This effect was again linked to copulation duration, with longer copulations less likely to lead to mating failure. While larger males tended to be more successful in sperm competition, especially if copulating second, female size had little effect on paternity, suggesting that cryptic male choice and sperm competition are acting relatively independently in this species.

Published
2024
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17. Is mating failure caused by cryptic male choice in the seed bug Lygaeus simulans?

Author

Vicki L. Balfour, Mélissa Armand, and David M. Shuker

Subjects
cryptic male choice, Lygaeus simulans, mate choice, mating failure, post‐copulatory sexual selection, sperm competition, Ecology, QH540-549.5
Abstract

Abstract One yet unresolved question in the study of mating system evolution is the occurrence of mating failure, when individuals go through their lives without successfully mating. This includes the failure to produce offspring even following copulation, for instance due to insemination or fertilisation failure. Copulations are costly in a variety of ways, but also a fundamental route to fitness in sexual species, and so we should expect that engaging in copulations that generate no offspring should be strongly selected against. Nonetheless, it has become apparent that mating failure is quite common in nature. Here we consider post‐copulatory sexual selection in Lygaeus simulans seed bugs to test the hypothesis that the high levels of mating failure found in this species (approximately 40%–60%) are caused by cryptic male choice (i.e. males choosing not to inseminate a female during copulation). In our first experiment, we found that mating failure depended on female size, but not male size, with smaller females experiencing mating failure more frequently. Mechanistically this is likely to be due to copulation duration, as shorter copulations were more likely to lead to mating failure. Likewise, copulations with smaller females were shorter. In our second and third experiments, rates of mating failure decreased when pairs were allowed to repeatedly interact with the same partner over longer durations (hours through to days), implying that mating failure is not primarily caused by infertility or chronic mechanical failure. Instead, our results strongly suggest cryptic male choice as the cause of mating failure in this species.

Published
2024
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18. The role of condition on sexual selection in the seed bug Lygaeus simulans

Author

Vicki L. Balfour, Mia K. Corliss, and David M. Shuker

Subjects
condition‐dependent, cryptic male choice, environmental stress, mate choice, mating failure, post‐copulatory sexual selection, Ecology, QH540-549.5
Abstract

Abstract Organism condition plays an important role in sexual selection. Sexual ornaments and displays can be condition‐dependent, reflecting either underlying genetic quality, experience of environmental stressors, or both. As such, the phenotypic expression of such traits, and the resulting patterns of mate choice acting on them, may be shaped by intrinsic genetic quality and the environment. Moreover, condition may also influence the choosing individual in mate choice, influencing their ability to invest in mate discrimination, or changing what traits of the chosen, including resources, are most preferred. Here we consider sexual selection and condition in the seed bug Lygaeus simulans, a species characterised by strong post‐copulatory sexual selection, but rather limited pre‐copulatory discrimination. We manipulated short‐term condition in both males and females by restricting access to water for 24 h. Water is particularly important in these bugs, given their feeding ecology and physiology. We found that water‐deprived males proved less likely to mate, while copulation duration with water‐deprived females was significantly reduced. Given the importance of copulation duration for the successful transfer of sperm by males to females, the data suggest cryptic male choice acting against water‐deprived females. These data add to those suggesting that cryptic male choice for fecund females plays an important role in sexual selection in this species. More generally, our results support the widespread importance of condition in terms of mating dynamics and sexual selection.

Published
2024
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19. Prospective antimicrobial stewardship interventions by multidisciplinary teams to reduce neonatal antibiotic use in South Africa: The Neonatal Antimicrobial Stewardship (NeoAMS) study

Author

Angela Dramowski, Pavel Prusakov, Debra A. Goff, Adrian Brink, Nelesh P. Govender, Ama Sakoa Annor, Liezl Balfour, Adrie Bekker, Azraa Cassim, Michelle Gijzelaar, Sandi L. Holgate, Sonya Kolman, Angeliki Messina, Hafsah Tootla, Natalie Schellack, Andriette van Jaarsveld, Kessendri Reddy, Shakti Pillay, Lucinda Conradie, Anika M. van Niekerk, Tarina Bester, Pearl Alexander, Antoinette Andrews, Magdel Dippenaar, Colleen Bamford, Sharnel Brits, Pinky Chirwa, Hannelie Erasmus, Pieter Ekermans, Pebenita Gounden, Teresa Kriel, Dini Mawela, Masego Moncho, Tonia Mphuthi, Ronald Nhari, Esmita Charani, Pablo J. Sánchez, and Dena van den Bergh

Subjects
Antibiotic, Antimicrobial stewardship programme, Neonate, Africa, Pharmacist, Multi-disciplinary, Infectious and parasitic diseases, RC109-216
Abstract

Background: Hospitalized neonates are vulnerable to infection and have high rates of antibiotic utilization. Methods: Fourteen South African neonatal units (seven public, seven private sector) assembled multidisciplinary teams involving neonatologists, microbiologists, pharmacists, and nurses to implement prospective audit and feedback neonatal antimicrobial stewardship (NeoAMS) interventions. The teams attended seven online training sessions. Pharmacists conducted weekday antibiotic prescription reviews in the neonatal intensive care unit and/or neonatal wards providing feedback to the clinical teams. Anonymized demographic and NeoAMS interventions data were aggregated for descriptive purposes and statistical analysis. Findings: During the 20-week NeoAMS intervention in 2022, 565 neonates were enrolled. Pharmacists evaluated seven hundred antibiotic prescription episodes; rule-out sepsis (180; 26%) and culture-negative sepsis (138; 20%) were the most frequent indications for antibiotic prescription. For infection episodes with an identified pathogen, only 51% (116/229) of empiric treatments provided adequate antimicrobial coverage. Pharmacists recommended 437 NeoAMS interventions (0·6 per antibiotic prescription episode), with antibiotic discontinuation (42%), therapeutic drug monitoring (17%), and dosing (15%) recommendations most frequent. Neonatal clinicians’ acceptance rates for AMS recommendations were high (338; 77%). Mean antibiotic length of therapy decreased by 24% from 9·1 to 6·9 days (0·1 day decrease per intervention week; P = 0·001), with the greatest decline in length of therapy for culture-negative sepsis (8·2 days (95% CI 5·7-11·7) to 5·9 days (95% CI 4·6-7·5); P = 0·032). Interpretation: This neonatal AMS programme was successfully implemented in heterogenous and resource-limited settings. Pharmacist-recommended AMS interventions had high rates of clinician acceptance. The NeoAMS intervention significantly reduced neonatal antibiotic use, particularly for culture-negative sepsis. Funding: A grant from Merck provided partial support.

Published
2024
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20. Characterization Of Inpaint Residuals In Interferometric Measurements of the Epoch Of Reionization

Author

Pagano, Michael, Liu, Jing, Liu, Adrian, Kern, Nicholas S., Ewall-Wice, Aaron, Bull, Philip, Pascua, Robert, Ravanbakhsh, Siamak, Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Burba, Jacob, Carey, Steven, Carilli, Chris L., Cheng, Carina, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Dillon, Joshua S., Eksteen, Nico, Ely, John, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Glendenning, Brian, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hazelton, Bryna J., Hewitt, Jacqueline N., Hickish, Jack, Jacobs, Daniel C., Julius, Austin, Kariseb, MacCalvin, Kerrigan, Joshua, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Loots, Anita, MacMahon, David Harold Edward, Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Morales, Miguel F., Mosiane, Tshegofalang, Neben, Abraham R., Nikolic, Bojan, Nuwegeld, Hans, Parsons, Aaron R., Patra, Nipanjana, Pieterse, Samantha, Razavi-Ghods, Nima, Robnett, James, Rosie, Kathryn, Sims, Peter, Smith, Craig, Swarts, Hilton, Thyagarajan, Nithyanandan, van Wyngaarden, Pieter, Williams, Peter K. G., and Zheng, Haoxuan

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

Radio Frequency Interference (RFI) is one of the systematic challenges preventing 21cm interferometric instruments from detecting the Epoch of Reionization. To mitigate the effects of RFI on data analysis pipelines, numerous inpaint techniques have been developed to restore RFI corrupted data. We examine the qualitative and quantitative errors introduced into the visibilities and power spectrum due to inpainting. We perform our analysis on simulated data as well as real data from the Hydrogen Epoch of Reionization Array (HERA) Phase 1 upper limits. We also introduce a convolutional neural network that capable of inpainting RFI corrupted data in interferometric instruments. We train our network on simulated data and show that our network is capable at inpainting real data without requiring to be retrained. We find that techniques that incorporate high wavenumbers in delay space in their modeling are best suited for inpainting over narrowband RFI. We also show that with our fiducial parameters Discrete Prolate Spheroidal Sequences (DPSS) and CLEAN provide the best performance for intermittent ``narrowband'' RFI while Gaussian Progress Regression (GPR) and Least Squares Spectral Analysis (LSSA) provide the best performance for larger RFI gaps. However we caution that these qualitative conclusions are sensitive to the chosen hyperparameters of each inpainting technique. We find these results to be consistent in both simulated and real visibilities. We show that all inpainting techniques reliably reproduce foreground dominated modes in the power spectrum. Since the inpainting techniques should not be capable of reproducing noise realizations, we find that the largest errors occur in the noise dominated delay modes. We show that in the future, as the noise level of the data comes down, CLEAN and DPSS are most capable of reproducing the fine frequency structure in the visibilities of HERA data., Comment: 21 pages, 13 figures

Published
2022
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21. Improved Constraints on the 21 cm EoR Power Spectrum and the X-Ray Heating of the IGM with HERA Phase I Observations

Author

The HERA Collaboration, Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Barkana, Rennan, Beardsley, Adam P., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Breitman, Daniela, Bull, Philip, Burba, Jacob, Carey, Steve, Carilli, Chris L., Cheng, Carina, Choudhuri, Samir, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Dillon, Joshua S., Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fialkov, Anastasia, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Garsden, Hugh, Glendenning, Brian, Gorce, Adélie, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hazelton, Bryna J., Heimersheim, Stefan, Hewitt, Jacqueline N., Hickish, Jack, Jacobs, Daniel C., Julius, Austin, Kern, Nicholas S., Kerrigan, Joshua, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Lewis, David, Liu, Adrian, Loots, Anita, Ma, Yin-Zhe, MacMahon, David H. E., Malan, Lourence, Malgas, Keith, Malgas, Cresshim, Maree, Matthys, Marero, Bradley, Martinot, Zachary E., McBride, Lisa, Mesinger, Andrei, Mirocha, Jordan, Molewa, Mathakane, Morales, Miguel F., Mosiane, Tshegofalang, Muñoz, Julian B., Murray, Steven G., Nagpal, Vighnesh, Neben, Abraham R., Nikolic, Bojan, Nunhokee, Chuneeta D., Nuwegeld, Hans, Parsons, Aaron R., Pascua, Robert, Patra, Nipanjana, Pieterse, Samantha, Qin, Yuxiang, Razavi-Ghods, Nima, Robnett, James, Rosie, Kathryn, Santos, Mario G., Sims, Peter, Singh, Saurabh, Smith, Craig, Swarts, Hilton, Tan, Jianrong, Thyagarajan, Nithyanandan, Wilensky, Michael J., Williams, Peter K. G., van Wyngaarden, Pieter, and Zheng, Haoxuan

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

We report the most sensitive upper limits to date on the 21 cm epoch of reionization power spectrum using 94 nights of observing with Phase I of the Hydrogen Epoch of Reionization Array (HERA). Using similar analysis techniques as in previously reported limits (HERA Collaboration 2022a), we find at 95% confidence that $\Delta^2(k = 0.34$ $h$ Mpc$^{-1}$) $\leq 457$ mK$^2$ at $z = 7.9$ and that $\Delta^2 (k = 0.36$ $h$ Mpc$^{-1}) \leq 3,496$ mK$^2$ at $z = 10.4$, an improvement by a factor of 2.1 and 2.6 respectively. These limits are mostly consistent with thermal noise over a wide range of $k$ after our data quality cuts, despite performing a relatively conservative analysis designed to minimize signal loss. Our results are validated with both statistical tests on the data and end-to-end pipeline simulations. We also report updated constraints on the astrophysics of reionization and the cosmic dawn. Using multiple independent modeling and inference techniques previously employed by HERA Collaboration (2022b), we find that the intergalactic medium must have been heated above the adiabatic cooling limit at least as early as $z = 10.4$, ruling out a broad set of so-called "cold reionization" scenarios. If this heating is due to high-mass X-ray binaries during the cosmic dawn, as is generally believed, our result's 99% credible interval excludes the local relationship between soft X-ray luminosity and star formation and thus requires heating driven by evolved low-metallicity stars., Comment: 57 pages, 37 figures. Updated to match the accepted ApJ version. Corresponding author: Joshua S. Dillon

Published
2022
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22. Impact of instrument and data characteristics in the interferometric reconstruction of the 21 cm power spectrum

Author

Gorce, Adélie, Ganjam, Samskruthi, Liu, Adrian, Murray, Steven G., Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Bull, Philip, Burba, Jacob, Carey, Steven, Carilli, Chris L., Cheng, Carina, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Dillon, Joshua S., Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Glendenning, Brian, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hazelton, Bryna J., Hewitt, Jacqueline N., Hickish, Jack, Jacobs, Daniel C., Julius, Austin, Kariseb, MacCalvin, Kern, Nicholas S., Kerrigan, Joshua, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Loots, Anita, MacMahon, David Harold Edward, Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Morales, Miguel F., Mosiane, Tshegofalang, Neben, Abraham R., Nikolic, Bojan, Nuwegeld, Hans, Parsons, Aaron R., Patra, Nipanjana, Pieterse, Samantha, Pober, Jonathan C., Razavi-Ghods, Nima, Robnett, James, Rosie, Kathryn, Sims, Peter, Smith, Craig, Swarts, Hilton, Thyagarajan, Nithyanandan, van Wyngaarden, Pieter, Williams, Peter K. G., and Zheng, Haoxuan

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Combining the visibilities measured by an interferometer to form a cosmological power spectrum is a complicated process. In a delay-based analysis, the mapping between instrumental and cosmological space is not a one-to-one relation. Instead, neighbouring modes contribute to the power measured at one point, with their respective contributions encoded in the window functions. To better understand the power measured by an interferometer, we assess the impact of instrument characteristics and analysis choices on these window functions. Focusing on the Hydrogen Epoch of Reionization Array (HERA) as a case study, we find that long-baseline observations correspond to enhanced low-k tails of the window functions, which facilitate foreground leakage, whilst an informed choice of bandwidth and frequency taper can reduce said tails. With simple test cases and realistic simulations, we show that, apart from tracing mode mixing, the window functions help accurately reconstruct the power spectrum estimator of simulated visibilities. The window functions depend strongly on the beam chromaticity, and less on its spatial structure - a Gaussian approximation, ignoring side lobes, is sufficient. Finally, we investigate the potential of asymmetric window functions, down-weighting the contribution of low-k power to avoid foreground leakage. The window functions presented here correspond to the latest HERA upper limits for the full Phase I data. They allow an accurate reconstruction of the power spectrum measured by the instrument and will be used in future analyses to confront theoretical models and data directly in cylindrical space., Comment: 18 pages, 19 figures, accepted for publication in MNRAS

Published
2022
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23. Investigating the causes of mating failure in Lygaeus simulans seed bugs

Author

Balfour, Vicki and Shuker, David M.

Subjects
Mating systems, Mating decisions, Lygaeus simulans, Cryptic male choice, Mating failure, Cryptic female choice, Reproductive interference, Sperm competition, Colour polymorphism, Pleiotropy, Sexual selection, Sperm precedence, Heterospecific, Hybridisation, Male mate choice, Mate choice, Insect reproduction, Cryptic mating failure, Lygaeus equestris, Post-copulatory sexual selection, Pre-copulatory sexual selection, Same sex sexual behaviour, Context-dependence, QL523.L9B2, Lygaeidae--Sexual behavior, Lygaeidae--Generative organs, Lygaeidae--Reproduction, Sexual selection in animals
Abstract

We should expect mating systems to evolve to maximise the relative fitness of individuals, i.e. through sexual selection acting on individuals to maximise the number of offspring they produce. However, some mating systems can appear to 'go wrong'. This is when apparently non-adaptive behavioural phenotypes, which cause fitness losses during reproduction, arise, such as same-sex sexual behaviours, reproductive interference, and mating failure. In this thesis I focus on the phenomenon of mating failure - when copulations fail to result in the production of offspring. Recorded levels of mating failure across taxa are non-trivial, and I here investigate the causes of mating failure in Lygaeus simulans seed bugs, a species known to suffer from high levels of failure (40-60%). I first investigated the genetics behind a pale mutant colour morph, which was inherited in a Mendelian fashion, providing a visible genetic marker for the investigation of post-copulatory selection processes. I found that mating failure caused extreme bimodality in second-male paternity, which could lead to misinterpretations of sperm competition mechanisms. I also found a strong link between copulation duration and mating failure, with longer copulations less likely to fail. Additionally, mating failure decreased when pairs were allowed to copulate for longer, or multiple times, indicating it is not primarily due to infertility or mechanical failures. Instead, evidence points towards mating failure being caused by cryptic male choice (CMC). In terms of post-copulatory outcomes, larger females were consistently more likely to lay eggs, have offspring (and hence not experience mating failure) and have more offspring. Males preferred to copulate, and copulate for longer, with larger females, suggesting CMC. Unfortunately, I was unsuccessful at teasing apart male and female effects to definitively demonstrate that mating failure is caused by CMC, but I believe the methods used could be useful in investigating CMC in the future.

Published
2023
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24. Associated SDOH needs of patients without health insurance and experiencing food insecurity

Author

Suma K. Thareja, Spenser Marting, William Davies, Santhosi Samudrala, Ramsey Rayes, Marie Balfour, Ana Mia Corujo-Ramirez, Frances Carter, Benjamin Liu, Dylan Trinh, Thomas Ritter, Jessica Miller, Coleman Fine, Rebecca Lundh, and Staci A. Young

Subjects
Food insecurity, Student-run free clinic, Free clinic, Disadvantaged populations, Preventative care, Medical education, Public aspects of medicine, RA1-1270, Social Sciences
Abstract

Abstract Although patients experiencing food insecurity commonly screen positive for a myriad of social determinants of health (SDOH) needs and chronic medical conditions influenced by diet, few studies have investigated associations within both uninsured and food insecure populations. We screened patients for food insecurity using the USDA six-item short form between October 2021 and April 2022. We then evaluated associations of food security status with nine separate SDOH needs and eight chronic medical conditions. In this cross-sectional study, of the 190 patients seen at a student-run free clinic serving patients without health insurance, 135 (71%) completed the SDOH survey. We identified chronic medical conditions via retrospective chart review and analyzed associations using multivariable logistic regressions adjusted for age and sex. Uninsured participants experiencing food insecurity (n = 22,16.3%) requested more support for: medications (adjusted odds ratio [AOR] = 7.28; 95% Confidence Interval [95% CI] = 2.33–23.2); p-value [P] =

Published
2024
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26. Cover

Author

Carolyn Côté-Lussier, David Moffette, Justin Piché, Gillian Balfour, Chris Bruckert, and Kathryn Campbell

Published
2020

27. Back Cover

Author

Carolyn Côté-Lussier, David Moffette, Justin Piché, Gillian Balfour, Chris Bruckert, and Kathryn Campbell

Published
2020

31. Title Page, Copyright

Author

Carolyn Côté-Lussier, David Moffette, Justin Piché, Gillian Balfour, Chris Bruckert, and Kathryn Campbell

Published
2020

33. Acknowledgements

Author

Carolyn Côté-Lussier, David Moffette, Justin Piché, Gillian Balfour, Chris Bruckert, and Kathryn Campbell

Published
2020

46. Direct Optimal Mapping for 21cm Cosmology: A Demonstration with the Hydrogen Epoch of Reionization Array

Author

Xu, Zhilei, Hewitt, Jacqueline N., Chen, Kai-Feng, Kim, Honggeun, Dillon, Joshua S., Kern, Nicholas S., Morales, Miguel F., Hazelton, Bryna J., Byrne, Ruby, Fagnoni, Nicolas, Acedo, Eloy de Lera, Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Bull, Philip, Burba, Jacob, Carey, Steven, Carilli, Chris L., Cheng, Carina, DeBoer, David R., Dexter, Matt, Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Glendenning, Brian, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hickish, Jack, Jacobs, Daniel C., Julius, Austin, Kariseb, MacCalvin, Kerrigan, Joshua, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Liu, Adrian, Loots, Anita, Ma, Yin-zhe, MacMahon, David Harold Edward, Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Mosiane, Tshegofalang, Murray, Steven G., Neben, Abraham R., Nikolic, Bojan, Nuwegeld, Hans, Parsons, Aaron R., Patra, Nipanjana, Pieterse, Samantha, Pober, Jonathan C., Razavi-Ghods, Nima, Robnett, James, Rosie, Kathryn, Sims, Peter, Smith, Craig, Swarts, Hilton, Thyagarajan, Nithyanandan, Van Van Wyngaarden, Pieter, Williams, Peter K. G., and Zheng, Haoxuan

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Motivated by the desire for wide-field images with well-defined statistical properties for 21cm cosmology, we implement an optimal mapping pipeline that computes a maximum likelihood estimator for the sky using the interferometric measurement equation. We demonstrate this direct optimal mapping with data from the Hydrogen Epoch of Reionization (HERA) Phase I observations. After validating the pipeline with simulated data, we develop a maximum likelihood figure-of-merit for comparing four sky models at 166MHz with a bandwidth of 100kHz. The HERA data agree with the GLEAM catalogs to <10%. After subtracting the GLEAM point sources, the HERA data discriminate between the different continuum sky models, providing most support for the model of Byrne et al. 2021. We report the computation cost for mapping the HERA Phase I data and project the computation for the HERA 320-antenna data; both are feasible with a modern server. The algorithm is broadly applicable to other interferometers and is valid for wide-field and non-coplanar arrays., Comment: 16 pages, 10 figures, 2 tables, published on ApJ

Published
2022
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48. Prospective antimicrobial stewardship interventions by multidisciplinary teams to reduce neonatal antibiotic use in South Africa: The Neonatal Antimicrobial Stewardship (NeoAMS) study

Author

Dramowski, Angela, Prusakov, Pavel, Goff, Debra A., Brink, Adrian, Govender, Nelesh P., Annor, Ama Sakoa, Balfour, Liezl, Bekker, Adrie, Cassim, Azraa, Gijzelaar, Michelle, Holgate, Sandi L., Kolman, Sonya, Messina, Angeliki, Tootla, Hafsah, Schellack, Natalie, van Jaarsveld, Andriette, Reddy, Kessendri, Pillay, Shakti, Conradie, Lucinda, van Niekerk, Anika M., Bester, Tarina, Alexander, Pearl, Andrews, Antoinette, Dippenaar, Magdel, Bamford, Colleen, Brits, Sharnel, Chirwa, Pinky, Erasmus, Hannelie, Ekermans, Pieter, Gounden, Pebenita, Kriel, Teresa, Mawela, Dini, Moncho, Masego, Mphuthi, Tonia, Nhari, Ronald, Charani, Esmita, Sánchez, Pablo J., and Bergh, Dena van den

Published
2024
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49. Automated Detection of Antenna Malfunctions in Large-N Interferometers: A Case Study with the Hydrogen Epoch of Reionization Array

Author

Storer, Dara, Dillon, Joshua S., Jacobs, Daniel C., Morales, Miguel F., Hazelton, Bryna J., Ewall-Wice, Aaron, Abdurashidova, Zara, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Balfour, Yanga, Beardsley, Adam P., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Bull, Philip, Burba, Jacob, Carey, Steven, Carilli, Chris L., Cheng, Carina, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Dynes, Scott, Ely, John, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Glendenning, Brian, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hewitt, Jacqueline N., Hickish, Jack, Huang, Tian, Josaitis, Alec, Julius, Austin, Kariseb, MacCalvin, Kern, Nicholas S., Kerrigan, Joshua, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Liu, Adrian, Loots, Anita, MacMahon, David, Malan, Lourence, Malgas, Cresshim, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Mosiane, Tshegofalang, Murray, Steven G., Neben, Abraham R., Nikolic, Bojan, Nunhokee, Chuneeta Devi, Parsons, Aaron R., Pascua, Robert, Patra, Nipanjana, Pieterse, Samantha, Pober, Jonathan C., Razavi-Ghods, Nima, Riley, Daniel, Robnett, James, Rosie, Kathryn, Santos, Mario G., Sims, Peter, Singh, Saurabh, Smith, Craig, Tan, Jianrong, Thyagarajan, Nithyanandan, Williams, Peter K. G., and Zheng, Haoxuan

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

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., Comment: 31 pages, 17 figures

Published
2021
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