A business case study for the Environmental information system for planners (EISP) : prepared under Memorandum of Understanding for the Department for Communities and Local Government

This report forms the deliverable for work led by the British Geological Survey (BGS) under a Memorandum of Understanding (MOU) with the Department of Communities and Local Government (DCLG) between 1st April 2007 and 31st October 2007. This work (Phase III) followed on from six years research effort (jointly funded by the Natural Environment Research Council URGENT Programme investment of £357,000 and the former Office of the Deputy Prime Minister, ODPM, investment of £347,000) (Phases I and II) in the development of an Environmental Information System for Planners (EISP). 2. Learning from the technically similar ODPM funded PARSOL-developed expert system, the costs of building production systems within a local planning authority are estimated. The availability and reasonable cost of nationally collated environmental datasets required to populate production EISPs, alongside the local authority provided data, are confirmed. The ‘off the shelf’ annual average cost to an individual Local Planning Authority considering to purchase and licence the data for such a production system is estimated at between £13,300 and £36,000 which compares well with other such types of IT systems purchased by LPAs in recent years. 3. Benefits to local authorities in using appropriate planning tools in EISP to implement DCLG environmental planning policies are estimated in terms of time and cost savings and actual extra environmental hazard costs avoided. Actual planning officer staff time saved using an EISP is estimated and costed and compared with the acquisition cost of such a commercially available production system. The saving is extremely conservatively estimated at £200,000 per year. This gives a conservative Benefit over Cost ratio of between 5.6-15 using staff time saving criteria alone. 4. A PARSOL-involved sample of local authorities, which were introduced to the likely costs and benefits of installing an EISP, concluded that it was definitely a worthwhile enhancement to eplanning. 5. Telford and Wrekin Council have offered to install a production EISP in 2008/9 with its technology consortium, if this can be funded by DCLG, as with the PARSOL expert systems. That system will be promoted throughout all the LPAs as the ‘Beacon’ system of best practice for Environmental Information Systems in Planning. 6. DCLG is recommended to fund the installation of one or two production EISP systems. One would be with the Telford and Wrekin Council system. The second would be with a local authority currently using CAP Solutions Uni-form planning system (basic e-planning infrastructure already installed in over 50% of English LPAs). These are costed at approximately £300,000 for the first system and £150,000 for the second

Exploration of intraclonal adaptation mechanisms of Pseudomonas brassicacearum facing cadmium toxicity

Pseudomonas brassicacearum forms phenotypic variants in vitro as well as in planta during root colonization under natural conditions, leading to subpopulations (phase I and II cells) that differ in colony morphology and production of exoenzymes/secondary metabolites. The maximal concentration of cadmium allowing both variants growth was 25 μM; however, phase II cells accumulated fivefold higher Cd than phase I cells, even though both variants showed the same growth rate and kinetics, comprising a long stasis period (50 h). The whole transcriptome analysis of both variants in response to Cd was investigated using the home-made DNA microarrays. This analysis revealed completely different adaptation mechanisms developed by each variant to withstand and grow in the presence of the toxic. A re-organization of the cell wall to limit Cd entrance was noticed for phase I cells, as genes encoding levan exopolymers were downregulated at the expense of an upregulation of genes encoding alginate, and an upregulation of transporters such as cadA, and a downregulation of copper transporters. Phase II cells were unable to prevent Cd entrance and recruited genes under the control of oxyR and soxR regulation to face osmotic and oxidant stresses generated by Cd. Putrescine and spermidine metabolism appeared to play a central role in Cd tolerance. Microarray data were validated by biological analyses such as motility, oxidative stress assay, metabolite profiling with ICR-FT/MS and UPLC, capillary electrophoresis analysis of biogenic amines

Non-Equilibrium Electron Transport in Two-Dimensional Nano-Structures Modeled by Green's Functions and the Finite-Element Method

We use the effective-mass approximation and the density-functional theory with the local-density approximation for modeling two-dimensional nano-structures connected phase-coherently to two infinite leads. Using the non-equilibrium Green's function method the electron density and the current are calculated under a bias voltage. The problem of solving for the Green's functions numerically is formulated using the finite-element method (FEM). The Green's functions have non-reflecting open boundary conditions to take care of the infinite size of the system. We show how these boundary conditions are formulated in the FEM. The scheme is tested by calculating transmission probabilities for simple model potentials. The potential of the scheme is demonstrated by determining non-linear current-voltage behaviors of resonant tunneling structures.Comment: 13 pages,15 figure

Special Supplemental Nutrition Program for Women, Infants, and Children Participant Grocery Store Purchases during the COVID-19 Pandemic in North Carolina

Background: Families participating in the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) experienced barriers to accessing healthy food during the COVID-19 pandemic, but we do not yet understand how WIC participant food purchases shifted during the pandemic. Objectives: We aimed to describe the association between the initial shock of the pandemic in March 2020 and WIC shoppers’ food purchases and changes in purchases before and during the pandemic at a top grocery chain and examine differences in these relationships by duration of WIC use. Methods: We used longitudinal food transaction data from WIC shoppers (n = 2,989,116 shopper-month observations from 175,081 unique WIC shoppers) from 496 stores in a top grocery store chain in North Carolina between October 2019 and May 2021. We used an interrupted time series design to describe the following: 1) the relationship between the initial shock of the pandemic and WIC shopper food purchases and 2) differences in purchases before and during the pandemic. To assess differences in purchases between shoppers consistently using WIC electronic benefit transfer (EBT) cards and shoppers starting or stopping WIC EBT use during the pandemic, we used models stratified by WIC group. Primary outcomes were share (%) of total calories purchased from fruits, vegetables, nuts, and legumes (FV), processed foods, and sugar-sweetened beverages (SSBs). Results: We observed small decreases in the share of total calories from FV (−0.4%) and small increases in the share of calories from processed food (1.1%) and SSBs (0.5%) purchased at this retailer when comparing the pre and post March 2020 periods. Compared with shoppers that started or stopped using WIC benefits during the pandemic, shoppers that used WIC benefits consistently had slightly higher FV and lower processed food and SSB purchases at this retailer. Conclusions: Future studies should examine whether additional supports for nutrient-dense food choices may be needed for families with low incomes in public health emergencies

Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas

Diet is associated with cancer prognosis, including head and neck cancer (HNC), and has been hypothesized to influence epigenetic state by determining the availability of functional groups involved in the modification of DNA and histone proteins. The goal of this study was to describe the association between pretreatment diet and HNC tumor DNA methylation. Information on usual pretreatment food and nutrient intake was estimated via food frequency questionnaire (FFQ) on 49 HNC cases. Tumor DNA methylation patterns were assessed using the Illumina Goldengate Methylation Cancer Panel. First, a methylation score, the sum of individual hypermethylated tumor suppressor associated CpG sites, was calculated and associated with dietary intake of micronutrients involved in one-carbon metabolism and antioxidant activity, and food groups abundant in these nutrients. Second, gene specific analyses using linear modeling with empirical Bayesian variance estimation were conducted to identify if methylation at individual CpG sites was associated with diet. All models were controlled for age, sex, smoking, alcohol and HPV status. Individuals reporting in the highest quartile of folate, vitamin B12 and vitamin A intake, compared with those in the lowest quartile, showed significantly less tumor suppressor gene methylation, as did patients reporting the highest cruciferous vegetable intake. Gene specific analyses identified differential associations between DNA methylation and vitamin B12 and vitamin A intake when stratifying by HPV status. These preliminary results suggest that intake of folate, vitamin A and vitamin B12 may be associated with the tumor DNA methylation profile in HNC and enhance tumor suppression

Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas

Diet is associated with cancer prognosis, including head and neck cancer (HNC), and has been hypothesized to influence epigenetic state by determining the availability of functional groups involved in the modification of DNA and histone proteins. The goal of this study was to describe the association between pretreatment diet and HNC tumor DNA methylation. Information on usual pretreatment food and nutrient intake was estimated via food frequency questionnaire (FFQ) on 49 HNC cases. Tumor DNA methylation patterns were assessed using the Illumina Goldengate Methylation Cancer Panel. First, a methylation score, the sum of individual hypermethylated tumor suppressor associated CpG sites, was calculated and associated with dietary intake of micronutrients involved in one-carbon metabolism and antioxidant activity, and food groups abundant in these nutrients. Second, gene specific analyses using linear modeling with empirical Bayesian variance estimation were conducted to identify if methylation at individual CpG sites was associated with diet. All models were controlled for age, sex, smoking, alcohol and HPV status. Individuals reporting in the highest quartile of folate, vitamin B12 and vitamin A intake, compared with those in the lowest quartile, showed significantly less tumor suppressor gene methylation, as did patients reporting the highest cruciferous vegetable intake. Gene specific analyses identified differential associations between DNA methylation and vitamin B12 and vitamin A intake when stratifying by HPV status. These preliminary results suggest that intake of folate, vitamin A and vitamin B12 may be associated with the tumor DNA methylation profile in HNC and enhance tumor suppression

Fermi acceleration in astrophysical jets

We consider the acceleration of energetic particles by Fermi processes (i.e., diffusive shock acceleration, second order Fermi acceleration, and gradual shear acceleration) in relativistic astrophysical jets, with particular attention given to recent progress in the field of viscous shear acceleration. We analyze the associated acceleration timescales and the resulting particle distributions, and discuss the relevance of these processes for the acceleration of charged particles in the jets of AGNs, GRBs and microquasars, showing that multi-component powerlaw-type particle distributions are likely to occur.Comment: 6 pages, one figure; based on talk at "The multimessenger approach to unidentified gamma-ray sources", Barcelona/Spain, July 2006; accepted for publication in Astrophysics and Space Scienc

Measurement of νˉμ\bar{\nu}_{\mu} and νμ\nu_{\mu} charged current inclusive cross sections and their ratio with the T2K off-axis near detector

We report a measurement of cross section $\sigma(\nu_{\mu}+{\rm nucleus}\rightarrow\mu^{-}+X)$ and the first measurements of the cross section $\sigma(\bar{\nu}_{\mu}+{\rm nucleus}\rightarrow\mu^{+}+X)$ and their ratio $R(\frac{\sigma(\bar \nu)}{\sigma(\nu)})$ at (anti-)neutrino energies below 1.5 GeV. We determine the single momentum bin cross section measurements, averaged over the T2K $\bar{\nu}/\nu$-flux, for the detector target material (mainly Carbon, Oxygen, Hydrogen and Copper) with phase space restricted laboratory frame kinematics of $\theta_{\mu}$500 MeV/c. The results are $\sigma(\bar{\nu})=\left( 0.900\pm0.029{\rm (stat.)}\pm0.088{\rm (syst.)}\right)\times10^{-39}$ and $\sigma(\nu)=\left( 2.41\ \pm0.022{\rm{(stat.)}}\pm0.231{\rm (syst.)}\ \right)\times10^{-39}$in units of cm$^{2}$/nucleon and$R\left(\frac{\sigma(\bar{\nu})}{\sigma(\nu)}\right)= 0.373\pm0.012{\rm (stat.)}\pm0.015{\rm (syst.)}$.Comment: 18 pages, 8 figure

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements