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"Burkholder, Rachel"
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The Arbovirus Mapping and Prediction (ArboMAP) system for West Nile virus forecasting
2024
Objectives
West Nile virus (WNV) is the most common mosquito-borne disease in the United States. Predicting the location and timing of outbreaks would allow targeting of disease prevention and mosquito control activities. Our objective was to develop software (ArboMAP) for routine WNV forecasting using public health surveillance data and meteorological observations.
Materials and Methods
ArboMAP was implemented using an R markdown script for data processing, modeling, and report generation. A Google Earth Engine application was developed to summarize and download weather data. Generalized additive models were used to make county-level predictions of WNV cases.
Results
ArboMAP minimized the number of manual steps required to make weekly forecasts, generated information that was useful for decision-makers, and has been tested and implemented in multiple public health institutions.
Discussion and Conclusion
Routine prediction of mosquito-borne disease risk is feasible and can be implemented by public health departments using ArboMAP.
Lay Summary
West Nile virus (WNV) is the most common mosquito-borne disease in the United States. To reduce the risk of WNV, public health agencies distribute information about how to avoid mosquito bites and use insecticides to reduce the abundances of disease-transmitting mosquitoes. Information about when and where the risk of getting WNV is highest would help these agencies to target their activities and use limited resources more efficiently. To support this goal, we developed the ArboMAP software system for predicting the risk of WNV disease in humans. ArboMAP uses information about recent weather combined with data obtained from trapping mosquitoes and testing them for presence of WNV to predict how many human cases will occur in future weeks. Predictions extend throughout the current WNV season (typically May-September) and are made for each county within a state. The system is implemented as a set of free software tools that can be used by epidemiologists in state and municipal departments of health. Feedback from public health agencies in South Dakota, Louisiana, Oklahoma, and Michigan has been incorporated to enhance the usability of the system and design visualizations that summarize the forecasts.
Journal Article
A Myth Retold: How “Till We Have Faces” confirms that a Myth is not a Fairytale
by
Burkholder, Rachel
in
American literature
,
British & Irish literature
,
British and Irish literature
2011
In the last fifty years or so, the study of myth and meaning has changed into the study of fairytales, and into world of non-meaning. But because myths are classified with fairytales, their depth and somber meaning are clouded with the various happy endings of fairytales. Myths, then, are stripped and analyzed the same way as fairytales, for critics do not perceive a distinction; therefore, when discussing modern fairytale criticism the conclusions are invariably applied to myths as well. Fairytales and myth suffer greatly from the modern views; both are lost in a world of criticism set on satisfying its own agenda. Literary criticism has stolen meaning out of words with deconstruction. Feminism rewrites the fairytales to liberate the women trapped in happily-ever-afters. Marxism blames the princes for being rich, turning any struggle into a social-economic statement. Such criticism and analysis leave out so much of what makes a fairytale a tale worth telling and a myth worth believing. It is as Tolkien said: fairy-stories (fairytales and myth) are more than just \"information\" and criticism as of late has looked only for the information and lost the wonder of the story that is being told. Because of the new definitions and their focus on Marxism, feminism, and psycho-analysis, and the older definitions that focus on meaning, function, and ritual, critics are confused as to where a work of literature such as Till We Have Faces should fit in. Is it a fairytale; is it a myth? Are the two mutually exclusive? Modern critics have argued that myth is a sub-category to the fairytale genre. While, studying the older critics is it obvious that myth is the greater literary form. In an attempt to come to terms with the new criticism and understand the old terms, the following case study has been developed.
Dissertation
Dynamics of the Storm Time Magnetopause and Magnetosheath Boundary Layers: An MMS‐THEMIS Conjunction
by
Burkholder, Brandon L.
,
Beedle, Jason
,
Gabrielse, Christine
in
Boundary layers
,
Convection
,
Earth
2024
This letter uses simultaneous observations from Magnetosphere Multiscale (MMS) and Time History of Events and Macroscale Interactions during Substorms (THEMIS) to address the dynamics of the magnetopause and magnetosheath boundary layers during the main phase of a storm during which the interplanetary magnetic field (IMF) reverses from south to north. Near the dawn terminator, MMS observes two boundary layers comprising open and closed field lines and containing energetic electrons and ring current oxygen. Some closed field line regions exhibit sunward convection, presenting an avenue to replenish dayside magnetic flux lost during the storm. Meanwhile, THEMIS observes two boundary layers in the pre‐noon sector which strongly resemble those observed at the flank by MMS. Observations from the three THEMIS spacecraft indicate the boundary layers are still evolving several hours after the IMF has turned northward. These observations advance our knowledge of the dynamic magnetopause and magnetosheath boundary layers under the combined effects of an ongoing storm and changing IMF. Plain Language Summary Earth's magnetic field, the magnetosphere, acts as a shield protecting the near Earth environment from the solar wind. During active times, this shield can be damaged and reduced in size, but during quieter times, the shield can expand and repair itself. This letter uses observations from multiple spacecraft to better understand how the edges of our magnetosphere change during the transition from active to more quiet times. We observe the development of boundary layers at the dayside and flanks of the magnetosphere. Convection in and around these layers can contribute to the growth of the magnetosphere after it has been eroded during active times. These observations also place limits on the size of the boundary layers and how quickly they may develop. Key Points Direct evidence of sunward transport of closed magnetic flux is observed by Magnetosphere Multiscale (MMS) at the dawn flank terminator MMS and Time History of Events and Macroscale Interactions during Substorms (THEMIS) observe nearly identical boundary layers at the dawn flank and pre‐noon sectors Boundary layers and sunward convecting flux tubes are populated with energetic electrons and ring current oxygen ions
Journal Article
Tyr1 phosphorylation promotes phosphorylation of Ser2 on the C-terminal domain of eukaryotic RNA polymerase II by P-TEFb
by
Irani, Seema
,
Mayfield, Joshua E
,
Mehaffey, M Rachel
in
Biochemistry and Chemical Biology
,
Chromatin
,
Data analysis
2019
The Positive Transcription Elongation Factor b (P-TEFb) phosphorylates Ser2 residues of the C-terminal domain (CTD) of the largest subunit (RPB1) of RNA polymerase II and is essential for the transition from transcription initiation to elongation in vivo. Surprisingly, P-TEFb exhibits Ser5 phosphorylation activity in vitro. The mechanism garnering Ser2 specificity to P-TEFb remains elusive and hinders understanding of the transition from transcription initiation to elongation. Through in vitro reconstruction of CTD phosphorylation, mass spectrometry analysis, and chromatin immunoprecipitation sequencing (ChIP-seq) analysis, we uncover a mechanism by which Tyr1 phosphorylation directs the kinase activity of P-TEFb and alters its specificity from Ser5 to Ser2. The loss of Tyr1 phosphorylation causes an accumulation of RNA polymerase II in the promoter region as detected by ChIP-seq. We demonstrate the ability of Tyr1 phosphorylation to generate a heterogeneous CTD modification landscape that expands the CTD’s coding potential. These findings provide direct experimental evidence for a combinatorial CTD phosphorylation code wherein previously installed modifications direct the identity and abundance of subsequent coding events by influencing the behavior of downstream enzymes. DNA contains the instructions for making proteins, which build and maintain our cells. So that the information encoded in DNA can be used, a molecular machine called RNA polymerase II makes copies of specific genes. These copies, in the form of a molecule called RNA, convey the instructions for making proteins to the rest of the cell. To ensure that RNA polymerase II copies the correct genes at the correct time, a group of regulatory proteins are needed to control its activity. Many of these proteins interact with RNA polymerase II at a region known as the C-terminal domain, or CTD for short. For example, before RNA polymerase can make a full copy of a gene, a small molecule called a phosphate group must first be added to CTD at specific units known as Ser2. The regulatory protein P-TEFb was thought to be responsible for phosphorylating Ser2. However, it was previously not known how P-TEFb added this phosphate group, and why it did not also add phosphate groups to other positions in the CTD domain that are structurally similar to Ser2. To investigate this, Mayfield, Irani et al. mixed the CTD domain with different regulatory proteins, and used various biochemical approaches to examine which specific positions of the domain had phosphate groups attached. These experiments revealed a previously unknown aspect of P-TEFb activity: its specificity for Ser2 increased dramatically if a different regulatory protein first added a phosphate group to a nearby location in CTD. This additional phosphate group directed P-TEFb to then add its phosphate specifically at Ser2. To confirm the activity of this mechanism in living human cells, Mayfield, Irani et al. used a drug that prevented the first phosphate from being added. In the drug treated cells, RNA polymerase II was found more frequently ‘stalled’ at positions on the DNA just before a gene starts. This suggests that living cells needs this two-phosphate code system in order for RNA polymerase II to progress and make copies of specific genes. These results are a step forward in understanding the complex control mechanisms cells use to make proteins from their DNA. Moreover, the model presented here – one phosphate addition priming a second specific phosphate addition – provides a template that may underlie similar regulatory processes.
Journal Article
Earth's Alfvén Wings Driven by the April 2023 Coronal Mass Ejection
by
Rice, Rachel
,
Wei, Hanying
,
Chen, Yuxi
in
Alfv & eacute
,
Alfvén wings
,
CME-magnetosphere interaction
2024
We report a rare regime of Earth's magnetosphere interaction with sub‐Alfvénic solar wind in which the windsock‐like magnetosphere transforms into one with Alfvén wings. In the magnetic cloud of a Coronal Mass Ejection (CME) on 24 April 2023, NASA's Magnetospheric Multiscale mission distinguishes the following features: (a) unshocked and accelerated low‐beta CME plasma coming directly against Earth's dayside magnetosphere; (b) dynamical wing filaments representing new channels of magnetic connection between the magnetosphere and foot points of the Sun's erupted flux rope; (c) cold CME ions observed with energized counter‐streaming electrons, evidence of CME plasma captured due to by reconnection between magnetic‐cloud and Alfvén‐wing field lines. The reported measurements advance our knowledge of CME interaction with planetary magnetospheres, and open new opportunities to understand how sub‐Alfvénic plasma flows impact astrophysical bodies such as Mercury, moons of Jupiter, and exoplanets close to their host stars. Plain Language Summary Like supersonically fast fighter jets creating sonic shocks in the air, planet Earth typically moves in the magnetized solar wind at super‐Alfvénic speeds and generates a bow shock. Here we report unprecedented observations of Earth's magnetosphere interacting with a sub‐Alfvénic solar wind brought by an erupted magnetic flux rope from the Sun, called a coronal mass ejection (CME). The terrestrial bow shock disappears, leaving the magnetosphere exposed directly to the cold CME plasma and the strong magnetic field from the Sun's corona. Our results show that the magnetosphere transforms from its typical windsock‐like configuration to having wings that magnetically connect our planet to the Sun. The wings are highways for Earth's plasma to be lost to the Sun, and for the plasma from the foot points of the Sun's erupted flux rope to access Earth's ionosphere. Our work indicates highly dynamic generation and interaction of the wing filaments, shedding new light on how sub‐Alfvénic plasma wind may impact astrophysical bodies in our solar and other stellar systems. Key Points MMS observed a rare regime of magnetosphere interaction with unshocked low‐beta CME plasma Wing filaments represent dynamical channels of magnetic connection between the magnetosphere and foot points of the Sun's erupted flux rope Cold CME ions observed on closed field lines, likely generated by dual‐wing reconnection
Journal Article
MMS Observations of a Compressed, Strongly Driven Magnetopause During the 2024 Mother's Day Storm
by
Fuselier, Stephen A
,
Sun, Weijie
,
Genestreti, Kevin J
in
Charged particles
,
Coronal mass ejection
,
Driving conditions
2025
From 10 to 12 May 2024, a series of coronal mass ejections led to one of the strongest geomagnetic storms of the century, referred to as the Mother's Day or Gannon Storm. MMS's position on the dayside magnetosphere on 11 May provided observations of a strongly driven and compressed ∼7RE $\\left(\\sim 7\\ {R}_{E}\\right)$ reconnecting magnetopause. Because of the driving conditions, the magnetopause became saturated with O+ ${O}^{+}$ outflows that dominated the mass density of the plasma environment. In the reconnecting magnetopause, MMS observes signatures of parallel electron heating on the magnetopause's magnetosheath side, but anomalous and significant electron cooling, especially from the perpendicular electron temperature on the magnetosphere side, possibly driven by additional mechanisms besides reconnection. Even with the strong driving and O+ ${O}^{+}$ outflows, we find an expected (0.19±0.04) $(0.19\\pm 0.04)$ normalized reconnection rate for the primary exhaust, indicating insensitivity to these conditions. The unnormalized rate, however, is atypically large and scales with the driving conditions.
Journal Article
Characterization of Ebola Virus–Associated Eye Disease
by
Davis, Bionca
,
Wallace, Augustine
,
Eghrari, Allen O.
in
Adult
,
Antibodies
,
Cicatrix - virology
2021
Survivors of Ebola virus disease (EVD) may experience ocular sequelae. Comparison with antibody-negative individuals from the local population is required to characterize the disease.
To assess features of ophthalmic disease specific to EVD.
This baseline cross-sectional analysis of survivors of EVD and their close contacts was conducted within PREVAIL III, a 5-year, longitudinal cohort study. Participants who enrolled at John F. Kennedy Medical Center in Liberia, West Africa from June 2015 to March 2016 were included in this analysis. Close contacts were defined as household members or sex partners of survivors of EVD. Data were analyzed from July 2016 to July 2020.
All participants, both survivors and close contacts, underwent testing of IgG antibody levels against Ebola virus surface glycoprotein.
Ocular symptoms, anterior and posterior ophthalmologic examination findings, and optical coherence tomography images were compared between antibody-positive survivors and antibody-negative close contacts.
A total of 564 antibody-positive survivors (320 [56.7%] female; mean [SD] age, 30.3 [14.0] years) and 635 antibody-negative close contacts (347 [54.6%] female; mean [SD] age, 25.8 [15.5] years) were enrolled in this study. Survivors were more likely to demonstrate color vision deficit (28.9% vs 19.0%, odds ratio [OR], 1.6; 95% CI, 1.2-2.1) and lower intraocular pressure (12.4 vs 13.5 mm Hg; mean difference, -1.2 mm Hg; 95% CI, -1.6 to -0.8 mm Hg) compared with close contacts. Dilated fundus examination revealed a higher percentage of vitreous cells (7.8% vs 0.5%; OR, 16.6; 95% CI, 5.0-55.2) and macular scars (4.6% vs 1.6%; OR, 2.8; 95% CI, 1.4-5.5) in survivors than in close contacts. Uveitis was present in 26.4% of survivors and 12.1% of close contacts (OR, 2.4; 95% CI, 1.8-3.2). Among all participants with uveitis, survivors were more likely than close contacts to have intermediate uveitis (34.2% vs 6.5% of all cases; OR, 7.8; 95% CI, 3.1-19.7) and had thicker mean central subfield thickness on optical coherence tomography (222 vs 212 μm; mean difference, 14.4 μm; 95% CI, 1.9-26.9 μm).
In this cross-sectional study, survivors of EVD had a distinct spectrum of ocular and neuro-ophthalmologic findings compared with close contacts that potentially require medical and surgical treatment.
Journal Article