Flooding and Inundation Modeling in the Great Bay Estuary

As part of this research, FVCOM, a finite-volume coastal ocean numerical hydrodynamic model (Chen, et al., 2003), was implemented into the Great Bay estuary. FVCOM is one of several community models that have been developed for coastal regions, and was selected because it utilizes an unstructured grid to discretize the model domain. The unstructured grid provides the ability to have fine scale resolution near the boundary or coastline and decreased resolution away from the boundary where the flow field is less complicated, resulting in greatly reduced computational expense in less dynamic regions allowing model runs to be completed in much shorter time periods. Grid development also requires that bathymetric data is accurately assigned to grid nodes in such a way that the model itself will be numerically stable. This requires significant development time implementing an appropriate grid mesh (Persson and Strang, 2004) with bathymetry data that has been smoothed to limit inherent numerical noise in the computations. FVCOM was implemented on a grid with finest resolution equaling 30 m, and then tested on a 10 day run with offshore forcing determined analytically by the 8 most energetic semi-diurnal (M2, N2, S2, K2) and diurnal (K1, O1, P1, Q1) tidal constituents at Fort Pt., NH (https://tidesandcurrents.noaa.gov/harcon.html?id=8423898), and including fresh water river fluxes from 6 rivers equivalent to 5 times the average daily discharge (Ward and Bub, 2007). The model was further tested utilizing the 100 year tropical storm event estimated from the North Atlantic Coast Comprehensive Study (NACCS; USACE, 2015), and the highest projected sea level rise scenario for year 2100 estimated by NOAA (http://www.corpsclimate.us/ccaceslcurves.cfm). The numerically stable model indicates that the grid can be used to simulate tidal forcing with maximum projected year storm surge and sea level rise in the Great Bay, and – with further development to include finer (10 m) mesh resolution and inclusion of surface waves and wind forcing – may be able to predict future flooding scenarios based on forecasted storm events and sea level rise

Inbreeding ratio and genetic relationships among strains of the Western clawed frog, Xenopus tropicalis

The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts

Intermediate reading exercises for use with the Durrell Analysis of Reading Difficulty.

Thesis (Ed.M.)--Boston Universit

Monitoring bioaerosol and odour emissions from composting facilities - WR1121

Government policy requires that valuable resources should be recovered and recycled from biodegradable waste. A successful and growing organics recycling industry delivers this policy with composting being one of the principal technologies deployed to process suitable feedstock such as garden and food waste. Composting inevitably generates bioaerosols – particulate matter comprising cells or cellular components that are released into the air as a result of disturbance of composting feedstock or the processing of final product. Exposure to bioaerosols has the potential to be harmful to human and animal health. The Environment Agency adopts a precautionary and risk-based approach to the regulation of composting facilities which was developed on the basis of research by Wheeler et al. (2001) and which has been updated as new evidence has become available. The Environment Agency also requires site operators to monitor bioaerosols around their facilities using methods specified in a standard protocol which relies upon classical microbiology methods which are tried and tested but which are labour-intensive, slow and offer only a snapshot view of a highly dynamic system. A recent IOM review commissioned by Defra (Searl, 2009) on exposure-response relationships for bioaerosol emissions from waste treatment processes identified significant gaps in knowledge of exposure to bioaerosols and recommended that more research was needed into alternatives to viable microbial monitoring such as priority biomarkers (notably endotoxin) and potential surrogates such as particulate matter. The IOM review also concluded that there is a lack of information to support the development of appropriate stand-off distances. The overall aim of this project was to provide evidence on bioaerosol production, dispersion and potential exposures from composting facilities in support of future developments in policy and regulation of biowaste facilities. The objectives were: (i) to undertake a comprehensive set of standard and novel bioaerosol measurements at representative composting sites to assess comparability between different methods and also to measure spatial and temporal variations; and (ii) to determine the odour emissions and then compare these with bioaerosol emissions to see if odour is a marker of significant bioaerosol exposure. Standard (AfOR, 2009) and novel (CEN filter method, endotoxin, glucan, qPCR, real-time particulates) bioaerosols measurements were taken on a minimum of three to a maximum of six occasions over a twelve month period at four different composting facilities in England. The composting facilities were selected to represent sites of varying sizes (tonnages) and to allow a comparison of bioaerosol concentrations at standard open windrow sites versus a fully-contained site. Additional supporting information was collected including meteorological data at the time of sampling, observation of site operations and measurements of odour at one of the sites. Supporting bioaerosol and odour dispersion modelling was conducted at the site where the odour measurements were made. The spatial trend of bioaerosol concentrations described by Wheeler et al., (1991) and upon which EA regulatory policy is based was broadly corroborated by this dataset. Excursions above the EA acceptable levels at or beyond 250m from source were rare. Bioaerosol concentrations at the enclosed site were generally lower than at the open windrow sites. There was no evidence of a seasonal pattern in bioaerosol concentrations at any of the sites whereas between-sampling day variations were apparent. The cause(s) of these variations were not identified. No consistent relationship was observed between the concentration of bioaerosols measured by the two AfOR standard methods. The two methods displayed certain strengths and weakness in different situations. The IOM sampling device proved to be better suited to situations where high bioaerosol concentrations were encountered (close to source); the Andersen proving to be more effective in the lower concentration range typically found upwind of a site or at distance downwind from source. The higher volume filtration device tested in this project (referred to as the CEN method) produced data that did not consistently match either of the AfOR standard methods. This device demonstrated greater sensitivity than the IOM filter method but suffered drawbacks associated with its weight and a lack of ease of use in the field. Endotoxin concentrations were normally below the level recommended by the Dutch Expert Committee on Occupational Safety but occasional exceedances of this standard were detected at the larger open windrow sites. The majority of glucan measurements were below a widely referred to 10ng/m3 threshold. Significantly elevated concentrations were detected at one of the larger open windrow sites. The dynamic range of the qPCR method is wider (4-5-log) than either of the AfOR and the CEN methods. It is also quicker to carry out and has the potential for automation. The results from the qPCR method are mainly higher than standard AfOR methods, as the method does not distinguish viable and non-viable spores. The spatial distribution of Aspergillus fumigatus spores (by qPCR) along sampling transects, gives similar results compared to AfOR (and CEN) methods. Real time particle detection showed that both TSP and PM10 are correlated to Aspergillus fumigatus spore concentration. No consistent relationship was observed between odour and bioaerosol concentrations (although this was a limited dataset). The envelope of modelled (back-extrapolated) bioaerosol emission rates straddles several orders of magnitude. Distinguishing the influences of meteorological conditions on this variability was not possible. It was not possible to predict bioaerosol or odour emission rates with confidence. This continues to hamper confidence in modelling of odours and bioaerosols from open windrow facilities. The findings of this research have implications for the current standard monitoring protocol which should be reviewed accordingly. The findings of this multi-site survey accord with existing regulatory policy and are supportive of the general trend towards enclosed facilities. Notwithstanding this, continuing research is needed to enhance the database on emission from bioaerosol and odour abatement technologies (e.g. biofilters); to determine the cause(s) of occasional bioaerosol peaks from open facilities; to improve exposure assessments through better modelling protocols; and to link enhanced exposure information to future health impact studies

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m6A from 3’ untranslated regions is associated with decreased relative transcript abundance and defective RNA 30 end formation. A functional consequence of disrupted m6A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of what their genomes encode

Measuring Redshift-Space Distortions using Photometric Surveys

We outline how redshift-space distortions (RSD) can be measured from the angular correlation function w({\theta}), of galaxies selected from photometric surveys. The natural degeneracy between RSD and galaxy bias can be minimized by comparing results from bins with top-hat galaxy selection in redshift, and bins based on the radial position of galaxy pair centres. This comparison can also be used to test the accuracy of the photometric redshifts. The presence of RSD will be clearly detectable with the next generation of photometric redshift surveys. We show that the Dark Energy Survey (DES) will be able to measure f(z){\sigma}_8(z) to a 1{\sigma} accuracy of (17 {\times} b)%, using galaxies drawn from a single narrow redshift slice centered at z = 1. Here b is the linear bias, and f is the logarithmic rate of change of the linear growth rate with respect to the scale factor. Extending to measurements of w({\theta}) for a series of bins of width 0.02(1 + z) over 0.5 < z < 1.4 will measure {\gamma} to a 1{\sigma} accuracy of 25%, given the model f = {\Omega}_m(z)^{\gamma}, and assuming a linear bias model that evolves such that b = 0.5 + z (and fixing other cosmological parameters). The accuracy of our analytic predictions is confirmed using mock catalogs drawn from simulations conducted by the MICE collaboration.Comment: Accepted by MNRAS, revisions include fixing of typos and clarification of the tex

Nutritional comparison of cooked fresh and frozen vegetables

Dietary antioxidants (AO) are believed to contribute to the overall health benefits seen from fruit and vegetables. Despite increased public awareness of the health benefits of fruit and vegetables through campaigns such as 5 A DAY, consumption remains low. Freezing is usually regarded as destructive to AO and ascorbic acid (AA) and this has fostered a belief that fresh vegetables are nutritionally superior to frozen. In this study, AO and AA activity in commercially bought fresh and frozen vegetables were investigated and compared after a typical home cooking practice (boiling). Five different vegetables were examined: carrots, broccoli, green beans, peas and spinach. Each vegetable was bought four times from a selection of local supermarkets and green grocers in the Wirral, United Kingdom to account for variation. The oxygen radical absorbance capacity (ORAC) assay and 2, 6-dichlorophenolindophenol (DCPIP) assay were utilised to measure total antioxidant capacity (TAC) and AA content respectively. The results showed both fresh and frozen vegetables to contain AO and AA after cooking. Cooked fresh spinach and peas contained significantly (p<.05) higher levels of total AO than cooked frozen spinach and peas. However the remaining fresh and frozen vegetables (broccoli, carrots and green beans) did not appear to differ in AO content after cooking. Furthermore there was no difference between AA content in fresh and frozen cooked vegetables. The current study provides evidence against the misconception that fresh is always nutritionally superior to frozen at the point of consumption. Frozen vegetable promotion may be the way forward to increase fruit and vegetable consumption as they are generally nutritionally comparable to fresh but, cheaper, result in less waste, are more convenient and, if packaged correctly, taste the same as fresh. Further work, on a larger scale, is needed, to measure AO and AA content of fresh and frozen vegetables bought and cooked by the consumer.Mushtaq, Sohai

Self Determination Theory and Health Behavior Interventions

Physical and mental health contribute to a person’s overall sense of well-being. People generally want to live happy and healthy lives, so they make decisions that will increase their well-being. Many factors contribute to our health, but health behavior is something we can modify. Health behavior interventions aim to promote healthy choices and a sense of well-being in patients. Interventions have a theoretical basis that influences the design of the intervention. Public health interventions have used self-determination theory (SDT) and its components to guide interventions that promote health behavior change in various populations. This paper will seek to understand the extent to which health interventions that incorporate SDT are successful in encouraging the behavior change they aim to promote. To situate SDT in a broader context, it will be compared to other behavior change theories. Applications of SDT in health behavior change and health support interventions will also be explored to better understand how SDT and how its components are used. Lastly, the limitations of the theory and its effectiveness will be discussed, in addition to the implications of the findings