Towards an Improved Neutrino Cross Section Landscape: First Measurements of ve-Argon and Monoenergetic v? Interactions

Knowledge of neutrino cross sections is critical for understanding neutrino oscillation experiments. Existing theoretical interaction models can be improved by data-driven constraints measured across a variety of neutrino-nucleus interaction mechanisms and energies. However, neutrino cross section measurements are complicated by a number of factors, including detector limitations and challenges to neutrino energy reconstruction. Improving neutrino flavor identification and reconstruction in now popular liquid argon time projection chamber (LArTPC) detectors operating with GeV-scale neutrino sources is critical for success in upcoming large-scale neutrino experiments like the Deep Underground Neutrino Experiment (DUNE), aiming to further illuminate our picture of the neutrino. Specifically, the value of the charge-parity violating phase governing neutrino mixing and the mass ordering of the neutrinos are yet unknown. In parallel, studies of unique known energy neutrinos from decays at rest can eliminate one source of uncertainty to improve our understanding of neutrino-nucleus interactions in the MeV range and aid detector energy calibration. The topics covered in this dissertation are broad. They traverse multiple collaborations, analysis, hardware tests, electron neutrinos, muon neutrinos, and photon detectors. Foremost are the two published results. The first is a measurement of the electron neutrino cross section on argon with ArgoNeuT (at the time the only measurement of its kind). This electron neutrino sample, albeit low in statistics, is unique as the only currently available GeV-scale neutrino beam electron neutrino data collected by a LArTPC. The GeV-scale energy region presents distinct challenges for electron neutrino identification and reconstruction driven by increased hadron multiplicities that obscure vertex information traditionally used to classify electron neutrinos. The ArgoNeuT analysis demonstrates novel strategies for GeV-scale electron neutrino searches. The second result is a measurement of monoenergetic muon neutrino interactions in MiniBooNE from kaon decay at rest in the NuMI neutrino beam dump. Neutrino energy reconstruction is famously difficult and this monoenergetic neutrino source is a valuable tool for probing neutrino-nucleus interactions. The distinct timing and direction information of these events make it possible to extract signal shape and rate above background and the resulting measurements can be used to constrain interaction models. Between these two bookends, we consider first MicroBooNE's low energy excess search and cross section program through the lens of the Wire-Cell tomographic reconstruction toolbox. And finally, we discuss photon detection in LArTPCs. The design and testing of the photon detection system for the Short Baseline Near Detector (SBND) and recent research and development efforts for DUNE are summarized.PHDPhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/169776/1/roryfitz_1.pd

Analysis and Prediction of the West African Monsoon Onset

The West African Monsoon onset marks a vital point in the seasonal monsoon cycle over the region with direct implications for local farmers and other stakeholders. In this work, valuable insight into the exact definition of the monsoon onset, its level of spatial consistency and cause of inter-annual variability of onsets has been presented. Criteria are presented to determine the value of monsoon onset definitions. There exist over seventeen unique onset definitions in publication. In this work, a representative sub-set of definitions have been compared to assess the relative value and suitability of onset definitions. It is found that the length scale over which a definition is defined determines the relevance to certain users. Local farmers require knowledge on local onset definitions which often have no similarity to regional onset definitions. Local onset dates are shown to have a pragmatic level of spatial homogeneity. Local Onset Regions (LORs) are presented over which local onset variability can be studied using a representative time series of onset dates. Using LORs, it is found that the seasonal progression of the Inter-Tropical Front and the phase of the Madden-Julian Oscillation drive the inter-annual variability of local onsets. The late passage of the Inter-Tropical Front past a LOR is linked to later onset in that region. Furthermore, when the Madden-Julian Oscillation inhibits convection across the Guinea Coast, local onset dates tend to be earlier than climatology. Further research into predicting drivers of local onset variability are suggested. Finally, seasonal forecast models tend to under-predict the variability of onset dates across West Africa. There is little significant correlation between observed onset dates (regional or local) and forecasts. It is concluded that seasonal onset forecasts are currently of little value to forecast users in West Africa. Suggestions as to the cause of this limitation are discussed

Assessing the level of spatial homogeneity of the agronomic Indian monsoon onset

Over monsoon regions, such as the Indian subcontinent, the local onset of persistent rainfall is a crucial event in the annual climate for agricultural planning. Recent work suggested that local onset dates are spatially coherent to a practical level over West Africa; a similar assessment is undertaken here for the Indian subcontinent. Areas of coherent onset, defined as local onset regions or LORs, exist over the studied region. These LORs are significant up to the 95% confidence interval and are primarily clustered around the Arabian Sea (adjacent to and extending over the Western Ghats), the Monsoon Trough (north central India), and the Bay of Bengal. These LORs capture regions where synoptic scale controls of onset may be present and identifiable. In other regions, the absence of LORs is indicative of regions where local and stochastic factors may dominate onset. A potential link between sea surface temperature anomalies and LOR variability is presented. Finally, Kerala, which is often used as a representative onset location, is not contained within an LOR suggesting that variability here may not be representative of wider onset variability

The vacuolar anti-Pseudomonal activity of neutrophil primary granule peptidyl-arginine deiminase enzymes

The role of neutrophils in host defense involves several cell processes including phagocytosis, degranulation of antimicrobial proteins, and the release of neutrophil extracellular traps (NETs). In turn, dysregulated cell activity is associated with the pathogenesis of airway and rheumatic diseases, in which neutrophil-derived enzymes including peptidyl-arginine deiminases (PADs) play a role. Known physiological functions of PADs in neutrophils are limited to the activity of PAD isotype 4 in histone citrullination in NET formation. The aim of this study was to extend our knowledge on the role of PADs in neutrophils and, specifically, bacterial killing within the confines of the phagocytic vacuole. Human neutrophils were fractionated by sucrose gradient ultracentrifuge and PADs localized in subcellular compartments by Western blot analysis. Direct interaction of PADs with Pseudomonas aeruginosa (P. aeruginosa) was assessed by flow cytometry and Western blot overlay. The participation of neutrophil PAD2 and PAD4 in killing of P. aeruginosa was assessed by inclusion of PAD-specific inhibitors. In vitro, bactericidal activity of recombinant human PAD2 or PAD4 enzymes against P. aeruginosa was determined by enumeration of colony-forming units (CFU). Together with neutrophil elastase (NE), PAD2 and PAD4 were localized to primary granules and, following activation with particulate stimuli, were degranulated in to the phagocytic vacuole. In vitro, PAD2 and PAD4 bound P. aeruginosa (p = 0.04) and significantly reduced bacterial survival to 49.1 ± 17.0 (p < 0.0001) and 48.5 ± 13.9% (p < 0.0001), respectively. Higher antibacterial activity was observed at neutral pH levels with the maximum toxicity at pH 6.5 and pH 7.5, comparable to the effects of neutrophil bactericidal permeability increasing protein. In phagosomal killing assays, inclusion of the PAD2 inhibitor, AFM-30a, or PAD4 inhibitor, GSK484, significantly increased survival of P. aeruginosa (AFM-30a, p = 0.05; and GSK484, p = 0.0079). Results indicate that PAD2 and PAD4 possess antimicrobial activity and are directly involved in the neutrophil antimicrobial processes. This study supports further research into the development of PAD-based antimicrobials

Breath Formate Is a Marker of Airway S-Nitrosothiol Depletion in Severe Asthma

-nitrosothiols (SNOs), a class of endogenous airway smooth muscle relaxants. This deficiency results from increased activity of an enzyme that both reduces SNOs to ammonia and oxidizes formaldehyde to formic acid, a volatile carboxylic acid that is more easily detected in exhaled breath condensate (EBC) than SNOs. We therefore hypothesize that depletion of airway SNOs is related to asthma pathology, and breath formate concentration may be a proxy measure of SNO catabolism. (r = −0.39, p = 0.002, asthmatics only), and positively correlated with the NO-derived ion nitrite (r = 0.46, p<0.0001) as well as with total serum IgE (r = 0.28, p = 0.016, asthmatics only). Furthermore, formate was not significantly correlated with other volatile organic acids nor with inhaled corticosteroid dose.-nitrosothiols

Impact of the Madden–Julian oscillation and equatorial waves on tracked mesoscale convective systems over southeast Asia

Southeast Asia is a region dominated by high-impact weather, but numerical weather prediction here is a challenge owing to the complex orography and interactions between small- and large-scale phenomena. Localised mesoscale convective systems (MCSs) can produce intense precipitation. Here, we track MCSs over a 5-year period in Himawari satellite data, characterise the distribution of MCSs in the region, and investigate how they are modulated by the Madden–Julian oscillation (MJO) and equatorial waves. Between 10°S and 10°N in southeast Asia, MCSs account for 45–70% of the precipitation during boreal extended winter (November–April). Over most of the region, the fractional MCS contribution to rainfall is higher than average on days with extreme rainfall (>55%). Long-lived (>12 hr) MCSs contribute disproportionately, providing 85% of the rainfall despite comprising only 34% of all MCSs. Variability in MCS rainfall accounts for >50% of the total rainfall variability during an MJO cycle, mostly due to larger numbers of MCSs in convectively active MJO phases. Variations in MCS size and mean rain rate due to shifts in the stratiform proportion provide compensating effects. In the west of the region, a shift to faster moving MCSs in active MJO phases and slower moving MCSs in inactive phases resulted in fast-moving MCSs having the greatest impact on the MJO-associated variability. Variability is larger in the west than in the east. Equatorial Kelvin waves modulate MCS rainfall, with MCSs accounting for 20–50% of local rainfall anomalies. This variability is again enhanced in the west. By contrast, rainfall anomalies due to westward-propagating mixed Rossby–gravity waves and Rossby-1 waves are dominated by tropical-cyclone-related rainfall. Skill at local scales may be extracted from forecasts of subseasonal drivers such as the MJO and Kelvin waves, by understanding how these modulate the number and characteristics of MCSs

The West African Monsoon Onset: a concise comparison of definitions

The onset of the West African Monsoon (WAM) marks a vital time for local and regional stakeholders. Whilst the seasonal progression of monsoon winds and the related migration of precipitation from the Guinea Coast towards the Soudan/Sahel is apparent, there exist contrasting man-made definitions of what the WAM onset means. Broadly speaking, onset can be analyzed regionally, locally or over a designated intermediate scale. There are at least eighteen distinct definitions of the WAM onset in publication with little work done on comparing observed onset from different definitions or comparing onset realizations across different datasets and resolutions. Here, nine definitions have been calculated using multiple datasets of different metrics at different resolution. It is found that mean regional onset dates are consistent across multiple datasets and different definitions. There is low inter-annual variability in regional onset suggesting that regional seasonal forecasting of the onset provides few benefits over climatology. In contrast, local onsets show high spatial, inter-annual and inter-definition variability. Furthermore it is found that there is little correlation between local onset dates and regional onset dates across West Africa implying a disharmony between regional measures of onset and the experience on a local scale. The results of this study show that evaluation of seasonal monsoon onset forecasts is far from straightforward. Given a seasonal forecasting model, it is possible to simultaneously have a good and bad prediction of monsoon onset simply through selection of onset definition and observational dataset used for comparison

Prospective study design and data analysis in UK Biobank

Population-based prospective studies, such as UK Biobank, are valuable for generating and testing hypotheses about the potential causes of human disease. We describe how UK Biobank's study design, data access policies, and approaches to statistical analysis can help to minimize error and improve the interpretability of research findings, with implications for other population-based prospective studies being established worldwide.</p

Global Spatial Risk Assessment of Sharks Under the Footprint of Fisheries

Effective ocean management and conservation of highly migratory species depends on resolving overlap between animal movements and distributions and fishing effort. Yet, this information is lacking at a global scale. Here we show, using a big-data approach combining satellite-tracked movements of pelagic sharks and global fishing fleets, that 24% of the mean monthly space used by sharks falls under the footprint of pelagic longline fisheries. Space use hotspots of commercially valuable sharks and of internationally protected species had the highest overlap with longlines (up to 76% and 64%, respectively) and were also associated with significant increases in fishing effort. We conclude that pelagic sharks have limited spatial refuge from current levels of high-seas fishing effort. Results demonstrate an urgent need for conservation and management measures at high-seas shark hotspots and highlight the potential of simultaneous satellite surveillance of megafauna and fishers as a tool for near-real time, dynamic management