Comprehensive environmental assessment: a meta-assessment approach.
Ontology highlight
ABSTRACT:
SUBMITTER: Powers CM
PROVIDER: S-EPMC3439956 | biostudies-other | 2012 Sep
REPOSITORIES: biostudies-other
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Project description:The Chinese government projected 30% of total consumed potatoes as a staple food (PSF) by 2020. We comprehensively assessed the potential impacts of PSF on rice and flour consumption, rice and wheat planting, energy and nutrient supply, irrigation-water, chemical nitrogen (N), phosphorus pentoxide (P2O5) and potassium oxide (K2O) fertilizer inputs and total greenhouse gases (GHG) emission for potatoes, rice and wheat, by assuming different proportions of potato substitutes for rice and flour. The results showed that per capita, 2.9 ± 0.3 and 4.7 ± 0.5 kg more potatoes per year would enter the Chinese staple-food diet, under the government's target. PSF consumed are expected to reach 5.2 ± 0.7 Tg yr-1, equivalent to substituting potatoes for 4.2 ± 0.8-8.5 ± 0.8 Tg yr-1 wheat and 5.1 ± 0.9-10.1 ± 1.8 Tg yr-1 rice under different scenarios. While this substitution can increase the nutrient supply index by 63% towards nutrient reference values, it may induce no significant effect on staple-food energy supply with lower chemical fertilizer (except for K2O) and irrigation-water inputs and GHG emissions in different substitution scenarios than the business as usual scenario. The reduction in rice and wheat demands lead to wheat in the North China Plain and early rice decrease by 6.1-11.4% and 12.1-24.1%, respectively. The total GHG reduction is equal to 1.1-9.0% of CO2 equivalent associated with CH4 and N2O emitted from the Chinese agroecosystem in 2005. The saved irrigation water for three crops compared to 2012 reaches the total water use of 17.9 ± 4.9-21.8 ± 5.9 million people in 2015. More N fertilizer, irrigation-water, and GHG can be reduced, if the PSF ratio is increased to 50% together with potato yield improves to the optimal level. Our results implied that the PSF policy is worth doing not only because of the healthier diets, but also to mitigate resource inputs and GHG emissions and it also supports agricultural structure adjustments in the areas of irrigated wheat on the North China Plain and early rice across China, designed to increase the adaptability to climate change.
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Project description:BACKGROUND:There is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing (NGS) that span the tree of life, comparing them with traditional biodiversity monitoring tools within ten 20×20 meter plots along a 700 meter elevational gradient. RESULTS:From six eDNA datasets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 109 NCBI taxonomy-defined phyla or equivalent, ranging from 31 to 60 for a given eDNA marker. Estimates of alpha and gamma diversity were sensitive to the number of sequence reads, whereas beta diversity estimates were less sensitive. The average within-plot beta diversity was lower than between plots for all markers. The soil beta diversity of COI and 18S markers showed the strongest response to the elevational variation of the eDNA markers (COI: r=0.49, p<0.001; 18S: r=0.48, p<0.001). Furthermore pairwise beta diversities for these two markers were strongly correlated with those calculated from traditional vegetation and invertebrate biodiversity measures. CONCLUSIONS:Using a soil-based eDNA approach, we demonstrate that standard phylogenetic markers are capable of recovering sequences from a broad diversity of eukaryotes, in addition to prokaryotes by 16S. The COI and 18S eDNA markers are the best proxies for aboveground biodiversity based on the high correlation between the pairwise beta diversities of these markers and those obtained using traditional methods.
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Project description:Parametric analysis of Cerebellar Ataxia (CA) could be of immense value compared to its subjective clinical assessments. This study focuses on a comprehensive scheme for objective assessment of CA through the instrumented versions of 9 commonly used neurological tests in 5 domains- speech, upper limb, lower limb, gait and balance. Twenty-three individuals diagnosed with CA to varying degrees and eleven age-matched healthy controls were recruited. Wearable inertial sensors and Kinect camera were utilised for data acquisition. Binary and multilabel discrimination power and intra-domain relationships of the features extracted from the sensor measures and the clinical scores were compared using Graph Theory, Centrality Measures, Random Forest binary and multilabel classification approaches. An optimal subset of 13 most important Principal Component (PC) features were selected for CA-control classification. This classification model resulted in an impressive performance accuracy of 97% (F1 score = 95.2%) with Holmesian dimensions distributed as 47.7% Stability, 6.3% Timing, 38.75% Accuracy and 7.24% Rhythmicity. Another optimal subset of 11 PC features demonstrated an F1 score of 84.2% in mapping the total 27 PC across 5 domains during CA multilabel discrimination. In both cases, the balance (Romberg) test contributed the most (31.1% and 42% respectively), followed by the peripheral tests whereas gait (Walking) test contributed the least. These findings paved the way for a better understanding of the feasibility of an instrumented system to assist informed clinical decision-making.
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Project description:We evaluated the suitability of high-throughput transcriptomics approach to monitor terrestrial ecosystems. Free-living Mus spretus from several polluted sites of Huelva (Andalusia, SW Spain) were compared with mice from Doñana Biological Reserve (“Santa Olalla” lagoon (SOL) used as negative control). As most popular bioindicators, M. spretus is poorly represented in gene databases, therefore limiting the use of genomics in ecotoxicological studies. To solve this problem, we used microarrays produced from mRNAs of M. musculus. Specifically we used the One-Color Gene Expression Platform commercialized by Agilent.
2013-12-31 | GSE33663 | GEO
Project description:We evaluated the suitability of high-throughput transcriptomics approach to monitor terrestrial ecosystems. Free-living Mus spretus from several polluted sites of Huelva (Andalusia, SW Spain) were compared with mice from DoM-CM-1ana Biological Reserve (M-bM-^@M-^\Santa OlallaM-bM-^@M-^] lagoon (SOL) used as negative control). As most popular bioindicators, M. spretus is poorly represented in gene databases, therefore limiting the use of genomics in ecotoxicological studies. To solve this problem, we used microarrays produced from mRNAs of M. musculus. Specifically we used the One-Color Gene Expression Platform commercialized by Agilent. Gene expression in Mus spretus liver was assessed in mice from 5 sites of the Spanish Southwest. Five independent experiments were performed. The arrays were hybridized with labelled cRNA samples made from pooled livers of 9 mice per sampling site. We made 4 technichal repetitions per sample.
2013-12-31 | E-GEOD-33663 | biostudies-arrayexpress
Project description:Environmental impact assessment (EIA) is used globally to manage the impacts of development projects on the environment, so there is an imperative to demonstrate that it can effectively identify risky projects. However, despite the widespread use of quantitative predictive risk models in areas such as toxicology, ecosystem modelling and water quality, the use of predictive risk tools to assess the overall expected environmental impacts of major construction and development proposals is comparatively rare. A risk-based approach has many potential advantages, including improved prediction and attribution of cause and effect; sensitivity analysis; continual learning; and optimal resource allocation. In this paper we investigate the feasibility of using a Bayesian belief network (BBN) to quantify the likelihood and consequence of non-compliance of new projects based on the occurrence probabilities of a set of expert-defined features. The BBN incorporates expert knowledge and continually improves its predictions based on new data as it is collected. We use simulation to explore the trade-off between the number of data points and the prediction accuracy of the BBN, and find that the BBN could predict risk with 90% accuracy using approximately 1000 data points. Although a further pilot test with real project data is required, our results suggest that a BBN is a promising method to monitor overall risks posed by development within an existing EIA process given a modest investment in data collection.
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Project description:Determining the influence of environmental factors on the stability of drugs is very helpful when choosing excipients, storage conditions or packaging materials. In addition, information about possible toxic degradation products enables detecting and avoiding the harmful side effects of the drug. We used the thin-layer chromatographic-densitometric procedure for the assay of five coxibs, conducted degradation studies in various environments and at different temperatures along with the determination of pharmacokinetic parameters. The results were subjected to chemometric analysis, to investigate and visualize the similarities and differences of the studied coxibs. Samples of the tested drug were also analyzed by UPLC-MS/MS in order to identify degradation products, and determine possible drug degradation pathways. Using the human liver cancer HepG2 cell line, the hepatotoxic effect of the degradation products was also determined. It was observed that all substances were relatively stable under the analyzed conditions and degraded more in acidic than alkaline environments. Robenacoxib is the drug that decomposes the fastest, and cimicoxib turned out to be the most stable. Robenacoxib also showed significant hepatotoxicity at the highest tested concentration, which correlates with the high degree of its degradation, and the probable formation of a more hepatoxic product. The obtained mass spectra of compounds formed as a result of hydrolysis of the protonated drug leading to the formation of several product ions, which enabled us to propose probable degradation pathways.
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Project description:IntroductionWe illustrate a comprehensive tampon safety assessment approach that assures products can be used safely. Material biocompatibility, vaginal mucosa assessment, vaginal microbiome evaluation, and in vitro assessment of potential risk of staphylococcal toxic shock syndrome expressed through growth of Staphylococcus aureus (S. aureus) and production of TSST-1 are the four essential portions of the approach. Post-marketing surveillance informs of possible health effects that warrant follow up. The approach meets or exceeds US and international regulatory guidance and is described through the example of four tampon products.Methods/resultsEach product is comprised mostly of large molecular weight components (cotton, rayon, polymers) that cannot pass the vaginal mucosa, are widely used across the industry, and replete with a vast body of safety data and a long history of safe use in the category. Quantitative risk assessment of all small molecular weight components assured a sufficient margin of safety supporting their use. Vaginal mucosa assessment confirmed that pressure points, rough edges and/or sharp contact points were absent. A randomized cross-over clinical trial (ClinicalTrials.gov Identifier: NCT03478371) revealed favorable comfort ratings, and few complaints of irritation, burning, stinging, or discomfort upon insertion, wear, and removal. Adverse events were few, mild in severity, self-limited and resolved without treatment. Vaginal microbiota assessment in vitro presented no adverse effect on microbial growth. Culture-independent microbiome analyses from vaginal swab samples obtained during the clinical trial showed no differences attributable to tampon usage, but instead due to statistically significant subject-to-subject variability. Growth of S. aureus and TSST-1 toxin production in the presence of any of the four products in vitro were statistically significantly reduced when compared to medium control alone.DiscussionThe data from the four elements of the comprehensive safety assessment approach illustrated herein confirm that tampons evaluated using this system can be used safely for menstrual protection. A post-marketing surveillance system that monitors and responds to in-market experiences indicated in-use tolerability of the product among consumers, thus confirming the conclusions of the pre-marketing safety assessment.
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Project description:Aim of the studyLiver regeneration is one of the essential fields of regenerative medicine as a branch of tissue engineering and molecular biology that draws global researchers' attention. This study aims to conduct a systematic review and meta-analysis on the high-throughput gene expression microarray dataset of liver regeneration on the NCBI-GEO database to identify the significant genes and signaling pathways and confirm the genes from literature studies on associated diseases.Material and methodsWe thoroughly searched the NCBI-GEO database to retrieve and screen the GEO microarray datasets' contents. Due to the inclusion of different species in eligible GEO datasets in the meta-analysis, the list of significant genes for the random-effects model were identified. Moreover, we carried out detailed gene analyses for three main gene ontology components and the KEGG signaling pathway. Furthermore, we investigated the possibility of genes' association with liver cancer through the Kaplan-Meier plot.ResultsThe random-effects model from six eligible GEO datasets identified 71 genes with eight down-regulated and 63 up-regulated genes. The target genes are involved in various cellular functions such as cell proliferation, cell death, and cell cycle control. Finally, we noted that 58 out of 71 genes are associated with different types of diseases related explicitly to other liver and inflammation diseases.ConclusionsThe current study assessed various GEO datasets at the early stages of liver regeneration with promising results. The present systematic review and meta-analysis results are beneficial for future novel drug design and discovery specifically for patients in the liver transplantation process.
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