Flood Extent and Volume Estimation using Multi-Temporal Synthetic Aperture Radar.

Ph. D. Thesis.Satellite imagery has the potential to monitor flooding across wide geographical regions. Recent launches have improved the spatial and temporal resolution of available data, with the European Space Agency (ESA) Copernicus programme providing global imagery at no end-user cost. Synthetic Aperture Radar (SAR) is of particular interest due to its ability to map flooding independent of weather conditions. Satellite-derived flood observations have real-world application in flood risk management and validation of hydrodynamic models. This thesis presents a workflow for estimating flood extent, depth and volume utilising ESA Sentinel-1 SAR imagery. Flood extents are extracted using a combination of change detection, variable histogram thresholding and object-based region growing. An innovative technique has been developed for estimating flood shoreline heights by combining the inundation extents with high-resolution terrain data. A grid-based framework is used to derive the water surface from the shoreline heights, from which water depth and volume are calculated. The methodology is applied to numerous catchments across the north of England that suffered from severe flooding throughout the winter of 2015-16. Extensive flooding has been identified throughout the study region, with peak inundation occurring on 29th December 2015. On this date, over 100 km2 of flooding is identified in the Ouse catchment, equating to a water volume of 0.18 km3. The SAR flood extents are validated against satellite optical imagery, achieving a Total Accuracy of 91% and a Critical Success Index of 77%. The derived water surfaces have an average error of 3 cm and an RMSE of 98 cm compared to river stage measurements. The methods developed are robust and globally applicable, shown with an additional study along the Mackenzie River in Australia. The presented methodology, alongside the increased temporal resolution provided by Sentinel-1, highlights the potential for accurate, reliable mapping of flood dynamics using satellite imagery.NERC, (DREAM) CD

Removal of calcium hydroxide from Weine Type II systems using photon-induced photoacoustic streaming, passive ultrasonic, and needle irrigation: a microcomputed tomography study

Objective This study compared the effectiveness of Er:YAG laser-activated irrigation (PIPS), passive ultrasonic irrigation (PUI) with EndoUltra and standard needle irrigation (SNI) in the removal of calcium hydroxide [Ca(OH)2] from the mesial roots of Weine Type II mandibular molars. Material and Methods Thirty mandibular molars were screened by µCT for the presence of mesial roots with complex intra-canal anatomy and a common apical foramen. The teeth were enlarged to a standardized 25/.06 preparation and filled with Ca(OH)2 paste. Specimens were divided into three groups (n=10) according to the technique used for Ca(OH)2 removal: PIPS, at 15 Hz and 20 mJ using a 9 mm long, 600 µm diameter tip; PUI using a 15/.02 tip; and SNI (30 Ga. side-vented needle). Equal volumes of 8.25% NaOCl and 17% EDTA were used in all groups. µCT was used to measure the initial amount of Ca(OH)2 present and to assess the residual volume of Ca(OH)2 following each irrigation protocol. Data were analyzed using Tukey HSD and Kruskal-Wallis tests (α=5%). Results The mean volume of Ca(OH)2 before removal was significantly higher in the coronal third than in the middle and apical third (p;0.05). PIPS (median 0%; IQR: 0-0) showed significant higher Ca(OH)2 removal in the apical third than PUI (median 100%, IQR: 85-100) and SNI (median 47%; IQR: 16-72) (

Post-transcriptional regulation of satellite cell quiescence by TTP-mediated mRNA decay.

Skeletal muscle satellite cells in their niche are quiescent and upon muscle injury, exit quiescence, proliferate to repair muscle tissue, and self-renew to replenish the satellite cell population. To understand the mechanisms involved in maintaining satellite cell quiescence, we identified gene transcripts that were differentially expressed during satellite cell activation following muscle injury. Transcripts encoding RNA binding proteins were among the most significantly changed and included the mRNA decay factor Tristetraprolin. Tristetraprolin promotes the decay of MyoD mRNA, which encodes a transcriptional regulator of myogenic commitment, via binding to the MyoD mRNA 3' untranslated region. Upon satellite cell activation, p38α/β MAPK phosphorylates MAPKAP2 and inactivates Tristetraprolin, stabilizing MyoD mRNA. Satellite cell specific knockdown of Tristetraprolin precociously activates satellite cells in vivo, enabling MyoD accumulation, differentiation and cell fusion into myofibers. Regulation of mRNAs by Tristetraprolin appears to function as one of several critical post-transcriptional regulatory mechanisms controlling satellite cell homeostasis

Agroforestry: Challenges and Opportunities in Rhino Camp and Imvepi Refugee Settlements of Arua District, Northern Uganda

In the past, the environment has been a low priority in humanitarian operations for refugee agencies and implementing partners because of the emergency context. However, actions to safeguard the environment can be undertaken concurrently with emergency interventions and organisations should take responsibility for conserving the environment in refugee settlements in the same way that they are responsible for the welfare of refugees. Tree-based interventions, such as agroforestry, have been demonstrated as a viable option for resilience and sustainability in landscapes with increasing human pressure. Refugee settlements are subject to intense human pressure and suffer environmental degradation as a consequence. The potential benefits of agroforestry in refugee settlements though are not well researched. This study explores the implementation of agroforestry schemes in refugee settlements in the Arua district of Uganda. Using semi-structured interviews with the beneficiaries of the International Centre for Research on Agroforestry (ICRAF) agroforestry projects in Imvepi and Rhino camps, the study identifies key benefits for participants and the environment. These include improved livelihoods and nutrition. However, there are challenges to overcome before agroforestry can be made more widely available in refugee camps. Key barriers include insufficient land, limited water availability and lack of local knowledge, which limits productivity. This research shows how relief, rehabilitation and development can work hand in hand to reduce social and environmental pressure in the targeted refugee settlements and host communities and improve the well-being of beneficiary households by creating opportunities for income generation, improving nutrition and contributing to social cohesion

Fiat: Deductive Synthesis of Abstract Data Types in a Proof Assistant

We present Fiat, a library for the Coq proof assistant supporting refinement of declarative specifications into efficient functional programs with a high degree of automation. Each refinement process leaves a proof trail, checkable by the normal Coq kernel, justifying its soundness. We focus on the synthesis of abstract data types that package methods with private data. We demonstrate the utility of our framework by applying it to the synthesis of query structures--abstract data types with SQL-like query and insert operations. Fiat includes a library for writing specifications of query structures in SQL-inspired notation, expressing operations over relations (tables) in terms of mathematical sets. This library includes a suite of tactics for automating the refinement of specifications into efficient, correct- by-construction OCaml code. Using these tactics, a programmer can generate such an implementation completely automatically by only specifying the equivalent of SQL indexes, data structures capturing useful views of the abstract data. Throughout we speculate on the new programming modularity possibilities enabled by an automated refinement system with proved-correct rules. “Every block of stone has a statue inside it and it is the task of the sculptor to discover it.”--MichelangeloNational Science Foundation (U.S.) (NSF grant CCF-1253229)United States. Defense Advanced Research Projects Agency (DARPA, agreement number FA8750-12-2- 0293

An evaluation of contaminated complete feed as a vehicle for porcine epidemic diarrhea virus infection of naïve pigs following consumption via natural feeding behavior: proof of concept

Background: Since its initial detection in May 2013, porcine epidemic diarrhea virus (PEDV) has spread rapidly throughout the US swine industry. Initially, contaminated feed was proposed as a risk factor for PEDV; however, data were not available to support this theory. Here we provide proof of concept of this risk by describing a novel means for recovering PEDV-contaminated complete feed material from commercial swine sites and conducting an in vivo experiment to prove its infectivity. Results: For on-farm detection of PEDV RNA in feed, paint rollers were used to collect material from at-risk feed bins from 3 clinically affected breeding herds. This material was tested by PCR and determined to be positive for PEDV-RNA (Ct = 19.50-22.20 range). To test infectivity, this material was pooled (Ct = 20.65) and a Treatment group of 3-week old PEDV-naïve piglets were allowed to consume it via natural feeding behavior. For the purpose of a Positive control, piglets were allowed to ingest feed spiked with stock PEDV (Ct = 18.23) while the negative control group received PEDV-free feed. Clinical signs of PEDV infection (vomiting and diarrhea) and viral shedding were observed in both the Positive control and Treatment group’ post-consumption with virus and microscopic lesions detected in intestinal samples No evidence of infection was observed in the Negative controls.Conclusions: These data provide proof of concept that contaminated complete feed can serve as a vehicle for PEDV infection of naïve pigs using natural feeding behavior

Quantitative study of rectangular waveguide behavior in the THz.

This report describes our efforts to quantify the behavior of micro-fabricated THz rectangular waveguides on a configurable, robust semiconductor-based platform. These waveguides are an enabling technology for coupling THz radiation directly from or to lasers, mixers, detectors, antennas, and other devices. Traditional waveguides fabricated on semiconductor platforms such as dielectric guides in the infrared or co-planar waveguides in the microwave regions, suffer high absorption and radiative losses in the THz. The former leads to very short propagation lengths, while the latter will lead to unwanted radiation modes and/or crosstalk in integrated devices. This project exploited the initial developments of THz micro-machined rectangular waveguides developed under the THz Grand Challenge Program, but instead of focusing on THz transceiver integration, this project focused on exploring the propagation loss and far-field radiation patterns of the waveguides. During the 9 month duration of this project we were able to reproduce the waveguide loss per unit of length in the waveguides and started to explore how the loss depended on wavelength. We also explored the far-field beam patterns emitted by H-plane horn antennas attached to the waveguides. In the process we learned that the method of measuring the beam patterns has a significant impact on what is actually measured, and this may have an effect on most of the beam patterns of THz that have been reported to date. The beam pattern measurements improved significantly throughout the project, but more refinements of the measurement are required before a definitive determination of the beam-pattern can be made

Evidence for a dominant-negative effect in ACTA1 nemaline myopathy caused by abnormal folding, aggregation and altered polymerization of mutant actin isoforms

We have studied a cohort of nemaline myopathy (NM) patients with mutations in the muscle α-skeletal actin gene (ACTA1). Immunoblot analysis of patient muscle demonstrates increased γ-filamin, myotilin, desmin and α-actinin in many NM patients, consistent with accumulation of Z line-derived nemaline bodies. We demonstrate that nebulin can appear abnormal secondary to a primary defect in actin, and show by isoelectric focusing that mutant actin isoforms are present within insoluble actin filaments isolated from muscle from two ACTA1 NM patients. Transfection of C2C12 myoblasts with mutant actinEGFP constructs resulted in abnormal cytoplasmic and intranuclear actin aggregates. Intranuclear aggregates were observed with V163L-, V163M- and R183G-actinEGFP constructs, and modeling shows these residues to be adjacent to the nuclear export signal of actin. V163L and V163M actin mutants are known to cause intranuclear rod myopathy, however, intranuclear bodies were not reported in patient R183G. Transfection studies in C2C12 myoblasts showed significant alterations in the ability of V136L and R183G actin mutants to polymerize and contribute to insoluble actin filaments. Thus, we provide direct evidence for a dominant-negative effect of mutant actin in NM. In vitro studies suggest that abnormal folding, altered polymerization and aggregation of mutant actin isoforms are common properties of NM ACTA1 mutants. Some of these effects are mutation-specific, and likely result in variations in the severity of muscle weakness seen in individual patients. A combination of these effects contributes to the common pathological hallmarks of NM, namely intranuclear and cytoplasmic rod formation, accumulation of thin filaments and myofibrillar disorganizatio

Evaluation of the benefits and risks of introducing Ebola community care centers, Sierra Leone.

In some parts of western Africa, Ebola treatment centers (ETCs) have reached capacity. Unless capacity is rapidly scaled up, the chance to avoid a generalized Ebola epidemic will soon diminish. The World Health Organization and partners are considering additional Ebola patient care options, including community care centers (CCCs), small, lightly staffed units that could be used to isolate patients outside the home and get them into care sooner than otherwise possible. Using a transmission model, we evaluated the benefits and risks of introducing CCCs into Sierra Leone's Western Area, where most ETCs are at capacity. We found that use of CCCs could lead to a decline in cases, even if virus transmission occurs between CCC patients and the community. However, to prevent CCC amplification of the epidemic, the risk of Ebola virus-negative persons being exposed to virus within CCCs would have to be offset by a reduction in community transmission resulting from CCC use

Role of the N*(1440) resonance in the pp->pnpi+ reaction

New measurement by CELSIUS-WASA Collaboration on the pp->pn pi+ reaction reveals clear evidence for the presence of the Roper resonance N*(1440) which has been ignored in previous theoretical calculations. In this article, based on an effective Lagrangian approach and available knowledge on the Roper resonance, we investigate the role of the Roper resonance for the pp->pn pi+ reaction. It is found that the contribution from the Roper resonance N*(1440) becomes significant for kinetic energy above 1.1 GeV, consistent with the new experimental observation. The t-channel sigma-meson exchange is dominant for the production of the Roper resonance.Comment: 13 pages, 4 figure