We present a statistical study of prominence and filament eruptions observed by the Atmospheric Imaging Assembly (AIA) aboard the Solar Dynamics Observatory (SDO). Several properties are recorded for ...904 events that were culled from the Heliophysics Event Knowledgebase (HEK) and incorporated into an online catalog for general use. These characteristics include the filament and eruption type, eruption symmetry and direction, apparent twisting and writhing motions, and the presence of vertical threads and coronal cavities. Associated flares and white-light coronal mass ejections (CME) are also recorded. Total rates are given for each property along with how they differ among filament types. We also examine the kinematics of 106 limb events to characterize the distinct slow- and fast-rise phases often exhibited by filament eruptions. The average fast-rise onset height, slow-rise duration, slow-rise velocity, maximum field-of-view (FOV) velocity, and maximum FOV acceleration are 83 Mm, 4.4 hours, 2.1 km/s, 106 km/s, and 111 m/s^2, respectively. All parameters exhibit lognormal probability distributions similar to that of CME speeds. A positive correlation between latitude and fast-rise onset height is found, which we attribute to a corresponding negative correlation in the average vertical magnetic field gradient, or decay index, estimated from potential field source surface (PFSS) extrapolations. We also find the decay index at the fast-rise onset point to be 1.1 on average, consistent with the critical instability threshold theorized for straight current channels. Finally, we explore relationships between the derived kinematics properties and apparent twisting motions. We find that events with evident twist have significantly faster CME speeds and significantly lower fast-rise onset heights, suggesting relationships between these values and flux rope helicity.
Detailed phenotyping is required to deepen our understanding of the biological mechanisms behind genetic associations. In addition, the impact of potentially modifiable risk factors on disease ...requires analytical frameworks that allow causal inference. Here, we discuss the characteristics of Recall-by-Genotype (RbG) as a study design aimed at addressing both these needs. We describe two broad scenarios for the application of RbG: studies using single variants and those using multiple variants. We consider the efficacy and practicality of the RbG approach, provide a catalogue of UK-based resources for such studies and present an online RbG study planner.
Vaccines against SARS-CoV-2 that induce mucosal immunity capable of preventing infection and disease remain urgently needed. In this study, we demonstrate the efficacy of Bordetella colonization ...factor A (BcfA), a novel bacteria-derived protein adjuvant, in SARS-CoV-2 spike-based prime-pull immunizations. We show that i.m. priming of mice with an aluminum hydroxide- and BcfA-adjuvanted spike subunit vaccine, followed by a BcfA-adjuvanted mucosal booster, generated Th17-polarized CD4+ tissue-resident memory T cells and neutralizing Abs. Immunization with this heterologous vaccine prevented weight loss following challenge with mouse-adapted SARS-CoV-2 (MA10) and reduced viral replication in the respiratory tract. Histopathology showed a strong leukocyte and polymorphonuclear cell infiltrate without epithelial damage in mice immunized with BcfA-containing vaccines. Importantly, neutralizing Abs and tissue-resident memory T cells were maintained until 3 mo postbooster. Viral load in the nose of mice challenged with the MA10 virus at this time point was significantly reduced compared with naive challenged mice and mice immunized with an aluminum hydroxide-adjuvanted vaccine. We show that vaccines adjuvanted with alum and BcfA, delivered through a heterologous prime-pull regimen, provide sustained protection against SARS-CoV-2 infection.
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•We investigated the prevalence of 13 honey bee-associated pathogens in honey bees (Apis mellifera) and 15 native bee and wasp species.•We found at least one honey bee-associated ...pathogen in 53 % of all native bees and wasps.•The most prevalent pathogens were Melissococcus plutonius, Nosema ceranae, deformed wing virus, and black queen cell virus.•Non-viral pathogens, notably M. plutonius and N. ceranae, are widely distributed in native bees and wasps.•M. plutonius and N. ceranae were often found at higher prevalence in native bee and wasp species than in honey bees.•Paenibacillus larvae was detected for the first time in a species other than A. mellifera, in a Xenoglossa spp. individual.
Pollinators have experienced significant declines in the past decade, in part due to emerging infectious diseases. Historically, studies have primarily focused on pathogens in the Western honey bee, Apis mellifera. However, recent work has demonstrated that these pathogens are shared by other pollinators and can negatively affect their health. Here, we surveyed honey bees and 15 native bee and wasp species for 13 pathogens traditionally associated with honey bees. The native bee and wasp species included 11 species not previously screened for pathogens. We found at least one honey bee-associated pathogen in 53% of native bee and wasp samples. The most widely distributed and commonly detected pathogens were the microsporidian Nosema ceranae, the bacterium Melissococcus plutonius, and the viruses deformed wing virus and black queen cell virus. The prevalence of viruses was generally higher in honey bees than in native bees and wasps. However, the prevalence of M. plutonius and the brood fungus Ascosphaera apis was significantly higher in some native bee species than in honey bees. The data also reveal novel trends in the association between co-occurring pathogens in honey bees and native bees and wasps at the pathogen community level. These results can inform the assessment of risks that native pollinator species face from pathogen stress, and indicate that many non-viral pathogens, notably M. plutonius and N. ceranae, are far more widely distributed and commonly found in native bees and wasps than previously thought.
Liquid chromatography-high-resolution mass spectrometry (LC-HRMS), as applied to untargeted metabolomics, enables the simultaneous detection of thousands of small molecules, generating complex ...datasets. Alignment is a crucial step in data processing pipelines, whereby LC-MS features derived from common ions are assembled into a unified matrix amenable to further analysis. Variability in the analytical factors that influence liquid chromatography separations complicates data alignment. This is prominent when aligning data acquired in different laboratories, generated using non-identical instruments, or between batches from large-scale studies. Previously, we developed metabCombiner for aligning disparately acquired LC-MS metabolomics datasets. Here, we report significant upgrades to metabCombiner that enable the stepwise alignment of multiple untargeted LC-MS metabolomics datasets, facilitating inter-laboratory reproducibility studies. To accomplish this, a "primary" feature list is used as a template for matching compounds in "target" feature lists. We demonstrate this workflow by aligning four lipidomics datasets from core laboratories generated using each institution's in-house LC-MS instrumentation and methods. We also introduce batchCombine, an application of the metabCombiner framework for aligning experiments composed of multiple batches. metabCombiner is available as an R package on Github and Bioconductor, along with a new online version implemented as an R Shiny App.
Abstract
Background
To inform prevention strategies, we assessed the extent of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and settings in which transmission occurred in ...a Georgia public school district.
Methods
During 1 December 2020–22 January 2021, SARS-CoV-2–infected index cases and their close contacts in schools were identified by school and public health officials. For in-school contacts, we assessed symptoms and offered SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR) testing; performed epidemiologic investigations and whole-genome sequencing to identify in-school transmission; and calculated secondary attack rate (SAR) by school setting (eg, sports, elementary school classroom), index case role (ie, staff, student), and index case symptomatic status.
Results
We identified 86 index cases and 1119 contacts, 688 (61.5%) of whom received testing. Fifty-nine of 679 (8.7%) contacts tested positive; 15 of 86 (17.4%) index cases resulted in ≥2 positive contacts. Among 55 persons testing positive with available symptom data, 31 (56.4%) were asymptomatic. Highest SARs were in indoor, high-contact sports settings (23.8% 95% confidence interval {CI}, 12.7%–33.3%), staff meetings/lunches (18.2% 95% CI, 4.5%–31.8%), and elementary school classrooms (9.5% 95% CI, 6.5%–12.5%). The SAR was higher for staff (13.1% 95% CI, 9.0%–17.2%) vs student index cases (5.8% 95% CI, 3.6%–8.0%) and for symptomatic (10.9% 95% CI, 8.1%–13.9%) vs asymptomatic index cases (3.0% 95% CI, 1.0%–5.5%).
Conclusions
Indoor sports may pose a risk to the safe operation of in-person learning. Preventing infection in staff members, through measures that include coronavirus disease 2019 vaccination, is critical to reducing in-school transmission. Because many positive contacts were asymptomatic, contact tracing should be paired with testing, regardless of symptoms.
We assessed severe acute respiratory syndrome coronavirus 2 transmission in a Georgia school district using in-depth epidemiologic investigations and whole-genome sequencing. In-school transmission occurred primarily when the index case was from an indoor sports setting, was a staff member, or had symptoms.
Field scouting is an important part of many research methodologies in plant pathology and plant phenomics. However, linking scouting data to field imagery is often hampered by the time‐consuming task ...of georeferencing with a GIS. Here, we present the QScout tool suite for integrating remote sensing imagery and raster data with field‐scouting data in QGIS, an open‐source GIS program. The central features of QScout are the Drop Pins and Locate Pins plugins, allowing the user to easily link scouted data to remote sensing imagery. QScout also includes the Value Grabber and Grid Aggregator plugins, which transfer raster data into pins and aggregate the data from the pins into a grid, respectively. The final tools, Drop, Grab, and Aggregate and Locate, Grab, and Aggregate, are plugins that combine subsets of the four core plugins. The interface allows GIS users to effectively make use of field‐scouted observations with remote imagery and can improve data organization, analysis, and identification of locations of interest for further scouting or targeted management. QScout is publicly available as a GitHub repository: (https://github.com/GoldLabGrapeSPEC/QScout).
Core Ideas
Linking remote sensing imagery to ground validation data is an essential first step in nearly all use‐cases.
Validation data are frequently not geo‐referenced, which makes connecting it to remote sensing data difficult and time consuming.
We have developed an open source tool that can help users easily link non‐georeferenced field data to raster and remote sensing imagery.
Our tool can improve data organization, analysis, and identification of locations of interest for investigation.
Abstract
Next-generation sequencing has resulted in an explosion of available data, much of which remains unstudied in terms of biochemical function; yet, experimental characterization of these ...sequences has the potential to provide unprecedented insight into the evolution of enzyme activity. One way to make inroads into the experimental study of the voluminous data available is to engage students by integrating teaching and research in a college classroom such that eventually hundreds or thousands of enzymes may be characterized. In this study, we capitalize on this potential to focus on SABATH methyltransferase enzymes that have been shown to methylate the important plant hormone, salicylic acid (SA), to form methyl salicylate. We analyze data from 76 enzymes of flowering plant species in 23 orders and 41 families to investigate how widely conserved substrate preference is for SA methyltransferase orthologs. We find a high degree of conservation of substrate preference for SA over the structurally similar metabolite, benzoic acid, with recent switches that appear to be associated with gene duplication and at least three cases of functional compensation by paralogous enzymes. The presence of Met in active site position 150 is a useful predictor of SA methylation preference in SABATH methyltransferases but enzymes with other residues in the homologous position show the same substrate preference. Although our dense and systematic sampling of SABATH enzymes across angiosperms has revealed novel insights, this is merely the “tip of the iceberg” since thousands of sequences remain uncharacterized in this enzyme family alone.
This study examined the efficacy of motivational interviewing (MI) for increasing physical activity in aging adults. Eighty-six participants aged 55 years and older were randomly assigned to receive ...either four weekly sessions of telephone-based MI for increasing physical activity, or a healthy activity living guide (information only control). Changes from baseline weekly caloric expenditure from physical activity, self-efficacy for physical activity, and stage of change for physical activity were compared across groups at posttreatment and six months follow-up. Results indicated that MI participants had higher weekly caloric expenditures from physical activity at posttreatment, but not at six months follow-up; higher self-efficacy for physical activity at six months follow-up; and demonstrated greater stage of change progression across assessments. These findings support the use of telephone-based MI for increasing physical activity in older adults in the short-term. Future studies will need to determine if follow-up booster sessions increase long-term efficacy.
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