Cross-hole seismic reflection surveying in coal measures

This thesis is concerned with the development of the cross-hole seismic reflection surveying method with particular application to the shallow Coal Measures strata found in opencast coal mining prospects in the U.K.A field acquisition technique developed for shallow boreholes utilising explosive sources and hydrophone receivers is described. Data have been acquired from several test sites in northern England. Data-processing techniques including wavefield separation and waveshaping deconvolution have been developed for cross-hole data and the theories behind these techniques are discussed. Methods of imaging cross-hole reflection data including the 'VSP-CDF transformation and Generalised Kirchhoff migration are applied to computer- generated synthetic data and to real data in order to yield a depth section of the seismic reflectivity between the boreholes. Finally, the data-processing and imaging techniques developed are applied to real data acquired at British Coal Opencast exploration sites in northern England between 1987 and 1990

The Receptor-Like Kinase SERK3/BAK1 Is Required for Basal Resistance against the Late Blight Pathogen Phytophthora infestans in Nicotiana benthamiana

BACKGROUND The filamentous oomycete plant pathogen Phytophthora infestans causes late blight, an economically important disease, on members of the nightshade family (Solanaceae), such as the crop plants potato and tomato. The related plant Nicotiana benthamiana is a model system to study plant-pathogen interactions, and the susceptibility of N. benthamiana to Phytophthora species varies from susceptible to resistant. Little is known about the extent to which plant basal immunity, mediated by membrane receptors that recognise conserved pathogen-associated molecular patterns (PAMPs), contributes to P. infestans resistance. PRINCIPAL FINDINGS We found that different species of Phytophthora have varying degrees of virulence on N. benthamiana ranging from avirulence (incompatible interaction) to moderate virulence through to full aggressiveness. The leucine-rich repeat receptor-like kinase (LRR-RLK) BAK1/SERK3 is a major modulator of PAMP-triggered immunity (PTI) in Arabidopsis thaliana and N. benthamiana. We cloned two NbSerk3 homologs, NbSerk3A and NbSerk3B, from N. benthamiana based on sequence similarity to the A. thaliana gene. N. benthamiana plants silenced for NbSerk3 showed markedly enhanced susceptibility to P. infestans infection but were not altered in resistance to Phytophthora mirabilis, a sister species of P. infestans that specializes on a different host plant. Furthermore, silencing of NbSerk3 reduced the cell death response triggered by the INF1, a secreted P. infestans protein with features of PAMPs. CONCLUSIONS/SIGNIFICANCE We demonstrated that N. benthamiana NbSERK3 significantly contributes to resistance to P. infestans and regulates the immune responses triggered by the P. infestans PAMP protein INF1. In the future, the identification of novel surface receptors that associate with NbSERK3A and/or NbSERK3B should lead to the identification of new receptors that mediate recognition of oomycete PAMPs, such as INF1.This work was supported by the Gatsby Charitable Foundation, BBSRC, Nuffield Foundation and the German Research Foundation (DFG). SS was supported by a personal research fellowship (SCHO1347/1-1). JPR is an Australian Research Council Future Fellow (FT0992129). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Urban-Focused Comprehensive Economic Development Strategy (CEDS)

This Comprehensive Economic Development Strategy (CEDS) is the outgrowth of a long running effort by the John S. Watson Institute for Public Policy at Thomas Edison State College (Watson Institute) to support economic and community development in New Jersey with a particular focus on urban areas in need of revitalization. The Watson Institute was previously awarded a United States Economic Development Administration (USEDA) grant to complete an economic analysis of the North Central New Jersey Region. The USEDA approved that analysis and awarded additional funds to continue our work, culminating in this CEDS plan. Several years ago, the Watson Institute recognized that there was an opportunity and need to engage in regional economic development planning and cooperation amongst members of the New Jersey Urban Mayors Association. Rapidly advancing technology and economies necessitate partnerships amongst local governments, non-profits, private firms, and universities to address broad economic development problems and reach long-term goals. Although many of the municipalities participating in the CEDS effort are not contiguous, they nonetheless share histories that have led to their current problems. Allowing geographic boundaries to limit the extent of opportunity is no longer a viable option for regions that want to see broad based and sustainable economic growth. The purpose of a CEDS is to bring together the public, non- profit, and private sectors to establish a comprehensive framework for economic growth and revitalization in a region. In this case, the “Region” is defined as 19 specific municipalities within a seven-county area of the state, including: Asbury Park, Bayonne, Bloomfield, East Orange, Elizabeth, Hoboken, Irvington, Jersey City, Lakewood, Neptune, New Brunswick, Newark, Orange, Passaic, Paterson, Perth Amboy, Plainfield, Roselle and Woodbridge. The geographic composition of this CEDS is unique in that the Region is not strictly speaking contiguous. What binds our Region together are the threads of common issues, opportunities, constraints, and the hope that, collectively, the communities can create solutions that would otherwise not be obtained individually. One of the most significant binding events of this region’s recent history is Superstorm Sandy. Minimizing disruption from natural disaster events is critical to any economic development goals and objectives of a community. There are a wide variety of reports and recommendations available to municipalities in helping them develop resiliency plans that are customized to meet the needs of their community. Discussions regarding resilient infrastructure have been an ongoing theme during this urban focused CEDS, and is reflected in several projects and initiatives focused on resiliency as well as it being a theme in projects that are not necessarily resiliency focused, but incorporate resiliency elements to reduce the stress put on other systems. Two of the more forward thinking projects included as part of resiliency strategies in this CEDS are the City of Hoboken’s flood wall and the Township of Woodbridge’s plan for a township wide microgrid. Although discussion about resiliency in general tends to focus on natural disaster, this CEDS discussion on resiliency also encompassed a wide variety of activities and topics. When at all possible, resilience focused projects should incorporate other resiliency related elements The steering committee met many times over the course of several years, for both the economic base analysis and for this CEDS plan. Steering committee members included representatives and officials from each community; non-profit organizations such as universities, community colleges, libraries and community-based organizations; and representatives of the private sector ranging from Fortune 100 corporations to small businesses. The steering committee’s work culminated in the Action Plan. The Action Plan serves as the roadmap that the Watson Institute, together with the New Jersey Urban Mayors Association and the CEDS steering committee itself, will use to implement sustainable economic development in the Region’s constituent municipalities. The challenges faced by the steering committee in formulating the CEDS plan were commensurate with those faced by each of the communities. The goals and objectives include: Enhancing, preserving and making resilient critical infrastructure assets; Promoting small business development; Addressing persistent and complex workforce issues; Marketing effectively to attract new businesses, residents and tourists; Promulgating best practices in economic development across all 19 communities; Providing adequate implementation assistance to execute the CEDS plan. The steering committee engaged in many planning exercises, including stakeholder and issues mapping, brainstorming, resource assessments, inventorying existing networks and programs, etc. The consulting team brought data, national economic development experience and certain stakeholder engagement techniques to elicit creative, non-linear thinking. The Watson Institute provided a Senior Fellow to meet and communicate with each community individually on multiple occasions to understand specific needs and encourage participation in the process. Following all these efforts, the steering committee agreed that, to be included in the CEDS plan, each action has to meet the following criteria: It must address one of the critical goals/objectives identified above, It must be realistic, clear and actionable, It must either require few local resources to implement or have a funding source identified, It must have a real and sustainable impact, and, It should be relatively short term to show progress and generate enthusiasm, It should be something that, if successful, can be quickly replicated across all 19 communities, It should have performance metrics that can be tracked and reported on. These criteria weighed considerably on the process and the steering committee’s deliberations. Unlike a “traditional” CEDS vested at the County or State level, with existing power structures and funding sources, this CEDS relies on the power of persuasion; the more effective utilization of existing resources; and the ability to realign stakeholders in a truly novel way

A distributed heat pulse sensor network for thermo-hydraulic monitoring of the soil subsurface

Fibre optic distributed temperature sensing (DTS) is used increasingly for environmental monitoring and subsurface characterization. Combined with heating of metal elements embedded within the fibre optic cable, the temperature response of the soil provides valuable information from which soil parameters such as thermal conductivity and soil moisture can be derived at high spatial and temporal resolution, and over long distances. We present a novel active distributed temperature sensing (A-DTS) system and its application to characterize spatial and temporal dynamics in soil thermal conductivity along a recently forested hillslope in Central England, UK. Compared with conventional techniques (needle probe surveys), A-DTS provided values with a similar spread although lower on average. The larger number of measurement points that A-DTS provides at higher spatial and temporal resolutions and the ability to repeat surveys under different meteorological or hydrological conditions allow for a more detailed examination of the spatial and temporal variability of thermal conductivities at the study site. Although system deployment time and costs are higher than with needle probes, A-DTS can be extremely appealing for applications requiring long-term monitoring, at high temporal repeatability, over long (kilometres) distances and with minimum soil disturbance, compared with one-off spatial surveys

Vascularized tissue‐engineered chambers promote survival and function of transplanted islets and improve glycemic control

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154402/1/fsb2fj054879fje.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154402/2/fsb2fj054879fje-sup-0001.pd

Comparative genomics profiling of clinical isolates of Aeromonas salmonicida using DNA microarrays

BACKGROUND: Aeromonas salmonicida has been isolated from numerous fish species and shows wide variation in virulence and pathogenicity. As part of a larger research program to identify virulence genes and candidates for vaccine development, a DNA microarray was constructed using a subset of 2024 genes from the draft genome sequence of A. salmonicida subsp. salmonicida strain A449. The microarray included genes encoding known virulence-associated factors in A. salmonicida and homologs of virulence genes of other pathogens. We used microarray-based comparative genomic hybridizations (M-CGH) to compare selected A. salmonicida sub-species and other Aeromonas species from different hosts and geographic locations. RESULTS: Results showed variable carriage of virulence-associated genes and generally increased variation in gene content across sub-species and species boundaries. The greatest variation was observed among genes associated with plasmids and transposons. There was little correlation between geographic region and degree of variation for all isolates tested. CONCLUSION: We have used the M-CGH technique to identify subsets of conserved genes from amongst this set of A. salmonicida virulence genes for further investigation as potential vaccine candidates. Unlike other bacterial characterization methods that use a small number of gene or DNA-based functions, M-CGH examines thousands of genes and/or whole genomes and thus is a more comprehensive analytical tool for veterinary or even human health research

The receptor-like kinase SERK3/BAK1 is required for basal resistance against the late blight pathogen phytophthora infestans in Nicotiana benthamiana.

BACKGROUND: The filamentous oomycete plant pathogen Phytophthora infestans causes late blight, an economically important disease, on members of the nightshade family (Solanaceae), such as the crop plants potato and tomato. The related plant Nicotiana benthamiana is a model system to study plant-pathogen interactions, and the susceptibility of N. benthamiana to Phytophthora species varies from susceptible to resistant. Little is known about the extent to which plant basal immunity, mediated by membrane receptors that recognise conserved pathogen-associated molecular patterns (PAMPs), contributes to P. infestans resistance. PRINCIPAL FINDINGS: We found that different species of Phytophthora have varying degrees of virulence on N. benthamiana ranging from avirulence (incompatible interaction) to moderate virulence through to full aggressiveness. The leucine-rich repeat receptor-like kinase (LRR-RLK) BAK1/SERK3 is a major modulator of PAMP-triggered immunity (PTI) in Arabidopsis thaliana and N. benthamiana. We cloned two NbSerk3 homologs, NbSerk3A and NbSerk3B, from N. benthamiana based on sequence similarity to the A. thaliana gene. N. benthamiana plants silenced for NbSerk3 showed markedly enhanced susceptibility to P. infestans infection but were not altered in resistance to Phytophthora mirabilis, a sister species of P. infestans that specializes on a different host plant. Furthermore, silencing of NbSerk3 reduced the cell death response triggered by the INF1, a secreted P. infestans protein with features of PAMPs. CONCLUSIONS/SIGNIFICANCE: We demonstrated that N. benthamiana NbSERK3 significantly contributes to resistance to P. infestans and regulates the immune responses triggered by the P. infestans PAMP protein INF1. In the future, the identification of novel surface receptors that associate with NbSERK3A and/or NbSERK3B should lead to the identification of new receptors that mediate recognition of oomycete PAMPs, such as INF1

Methods of a national colorectal cancer cohort study: the PIPER Project

A national study looking at bowel cancer in New Zealand has previously been completed (the PIPER Project). The study included 5,610 patients and collected medical information about how each person was found to have bowel cancer and the treatment they received. This paper reports how the study was carried out. The information collected in the study will be used to look at the quality of care being provided to New Zealand patients with bowel cancer, and to find out if differences in care occur based on where people live, their ethnicity and their socioeconomic status

First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

The description of genetic population structure over a species\u27 geographic range can provide insights into its evolutionary history and also support effective management efforts. Assessments for globally distributed species are rare, however, requiring significant international coordination and collaboration. The global distribution of demographically discrete populations for the humpback whale Megaptera novaeangliae is not fully known, hampering the definition of appropriate management units. Here, we present the first circumglobal assessment of mito - chondrial genetic population structure across the species\u27 range in the Southern Hemisphere and Arabian Sea. We combine new and existing data from the mitochondrial (mt)DNA control region that resulted in a 311 bp consensus sequence of the mtDNA control region for 3009 individuals sampled across 14 breeding stocks and subpopulations currently recognized by the International Whaling Commission. We assess genetic diversity and test for genetic differentiation and also estimate the magnitude and directionality of historic matrilineal gene flow between putative populations. Our results indicate that maternally directed site fidelity drives significant genetic population structure between breeding stocks within ocean basins. However, patterns of connectivity differ across the circumpolar range, possibly as a result of differences in the extent of longitudinal movements on feeding areas. The number of population comparisons observed to be significantly differentiated were found to diminish at the subpopulation scale when nucleotide differences were examined, indicating that more complex processes underlie genetic structure at this scale. It is crucial that these complexities and uncertainties are afforded greater consideration in management and regulatory efforts