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  • Elsevier  (232)
  • Oxford University Press  (56)
  • BioMed Central  (37)
  • Nature Publishing Group (NPG)
  • 2010-2014  (337)
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  • 1
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Environmental Management 146 (2014): 206-216, doi:10.1016/j.jenvman.2014.07.002.
    Description: Harmful algal blooms (HABs) are thought to be increasing in coastal waters worldwide. Anthropogenic nutrient enrichment has been proposed as a principal causative factor of this increase through elevated inorganic and/or organic nutrient concentrations and modified nutrient ratios. We assess: 1) the level of understanding of the link between the amount, form and ratio of anthropogenic nutrients and HABs; 2) the evidence for a link between anthropogenically generated HABs and negative impacts on human health; and 3) the economic implications of anthropogenic nutrient/HAB interactions. We demonstrate that an anthropogenic nutrient-HAB link is far from universal, and where it has been demonstrated, it is most frequently associated with high biomass rather than low biomass (biotoxin producing) HABs. While organic nutrients have been shown to support the growth of a range of HAB species, insufficient evidence exists to clearly establish if these nutrients specifically promote the growth of harmful species in preference to benign ones, or if/how they influence toxicity of harmful species. We conclude that the role of anthropogenic nutrients in promoting HABs is site-specific, with hydrodynamic processes often determining whether blooms occur. We also find a lack of evidence of widespread significant adverse health impacts from anthropogenic nutrient-generated HABs, although this may be partly due to a lack of human/animal health and HAB monitoring. Detailed economic evaluation and cost/benefit analysis of the impact of anthropogenically generated HABs, or nutrient reduction schemes to alleviate them, is also frequently lacking.
    Description: The work described here is based in part on a project ‘Harmful Algae, Nuisance Blooms and Anthropogenic Nutrient Enrichment’ funded by the UK Department for Environment, Food and Rural Affairs (contract ME2208). In addition KD was supported by the FP7 project Asimuth and funding from the NERC Shelf Seas Biogeochemistry and PURE Associates programmes. PJH was supported by University Grants Council of Hong Kong AoE project (AoE/P-04/0401). PH and LEF were funded by the US National Science Foundation (NSF) Award 1009106; LEF was funded in part by the European Regional Development Fund and European Social Fund (University of Exeter, Truro, Cornwall, UK). GM was supported by a NERC PhD studentship.
    Keywords: Harmful algal blooms ; HABs ; Anthropogenic nutrients ; Human health ; Economic impact
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 2
    Publication Date: 2013-09-07
    Description: Background: While efforts to improve cancer outcomes have typically focused on improving quality of care, recently, a growing emphasis has been placed on timely access to quality cancer care. This retrospective cohort study examines, at a population level, the relationship between quality and timeliness of colorectal cancer (CRC) care in a single Canadian province (Nova Scotia). Through the provincial cancer registry, we identified all residents diagnosed with invasive CRC between 2001 and 2005 that underwent a non-emergent resection. Using anonymized administrative databases that are individually linked at the patient level, we obtained clinicodemographic, diagnostic, and treatment event data. Selected charts were reviewed to ensure completeness of chemotherapy data.Performance on six quality indicators and the percentage of patients achieving wait time benchmarks for diagnosis, surgery, and adjuvant therapy were calculated. The relationship between quality indicators and wait time intervals was examined using logistic regression. Results: Where an association was identified, patients who received 'higher quality care' had longer wait times. Individuals who received a complete preoperative colonoscopy were less likely to meet benchmarks for time from presentation to diagnosis and from diagnosis to surgery. Those who received an appropriate radiation oncology consultation were less likely to meet benchmarks for time from diagnosis to surgery and from surgery to adjuvant therapy. Conclusions: As governments and other organizations move forward with strategies to reduce wait times, they must also focus on how to define and monitor quality care, and consider the relationship between these two dimensions of health care. Similarly, when developing quality improvement initiatives, the impact on resource utilization and potential to create longer waits for care must be considered.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 3
    Publication Date: 2014-12-14
    Description: Background: Most PCR-based diagnostics are still considered time- and labor-intensive due to disparate purification, amplification, and detection steps. Advancements in PCR enzymes and buffer chemistry have increased inhibitor tolerance, facilitating PCR directly from crude samples. Obviating the need for DNA purification, while lacking a concentration step, these direct sample methods are particularly apt for human genetic testing. However, direct PCR protocols have traditionally employed thermal cyclers with slow ramp rates and conservative hold times that significantly increase an assay?s time-to-result. For this proof-of-principle study, our objective was to significantly reduce sample preparation and assay time for a PCR-based genetic test, for myotonic dystrophy type 1 (DM1), by pairing an inhibitor-resistant enzyme mix with a rapid thermal cycler to analyze samples directly in whole blood. Methods: DM1 genetic screening was done with an adapted conventional PCR approach that employed the Streck Philisa? Thermal Cycler, the inhibitor-resistant NEBNext? High-Fidelity 2X PCR Master Mix, and agarose gel electrophoresis or an Agilent 2100 Bioanalyzer for detection. The Gene Link? Myotonic Dystrophy Genemer? Kit was used as a reference assay kit to evaluate the rapid assay. Results: In this work, a rapid and direct PCR assay testing 10% whole blood as template has been developed as an exclusionary screening assay for DM1, a triple-repeat genetic disorder. PCR amplification was completed in 15 minutes using 30 cycles, including in situ hot-start/cell lysis. Out of the 40 donors screened, this assay identified 23 (57.5%) as DM1 negative suggesting no need for further testing. These data are 100% concordant with data collected using the commercially available Gene Link Genemer? Kit per the kit-specific PCR protocol. Conclusions: The PCR assay described in this study amplified DM1 short tandem repeats in 15 minutes. By eliminating sample purification and slower conventional PCR protocols, we demonstrated how adaptation of current PCR technology and chemistries can produce a simple-to-use exclusionary screening assay that is independent of up-front sample prep, improving a clinical lab technician?s time-to-result. We envision this direct and rapid methodology could be applied to other conventional PCR-based genetic tests and sample matrices where genomic DNA is targeted for analysis within a given molecular diagnostic platform.
    Electronic ISSN: 1471-2350
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 4
    Publication Date: 2012-06-01
    Print ISSN: 1359-6462
    Electronic ISSN: 1872-8456
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Elsevier
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  • 5
    Publication Date: 2012-11-16
    Description: Background: The pig is a biomedical model to study human and livestock traits. Many of these traits are controlled by neuropeptides that result from the cleavage of prohormones by prohormone convertases. Only 45 prohormones have been confirmed in the pig. Sequence homology can be ineffective to annotate prohormone genes in sequenced species like the pig due to the multifactorial nature of the prohormone processing. The goal of this study is to undertake the first complete survey of prohormone and prohormone convertases genes in the pig genome. These genes were functionally annotated based on 35 gene expression microarray experiments. The cleavage sites of prohormone sequences into potentially active neuropeptides were predicted. Results: We identified 95 unique prohormone genes, 2 alternative calcitonin-related sequences, 8 prohormone convertases and 1 cleavage facilitator in the pig genome 10.2 assembly and trace archives. Of these, 11 pig prohormone genes have not been reported in the UniProt, UniGene or Gene databases. These genes are intermedin, cortistatin, insulin-like 5, orexigenic neuropeptide QRFP, prokineticin 2, prolactin-releasing peptide, parathyroid hormone 2, urocortin, urocortin 2, urocortin 3, and urotensin 2-related peptide. In addition, a novel neuropeptide S was identified in the pig genome correcting the previously reported pig sequence that is identical to the rabbit sequence. Most differentially expressed prohormone genes were under-expressed in pigs experiencing immune challenge relative to the un-challenged controls, in non-pregnant relative to pregnant sows, in old relative to young embryos, and in non-neural relative to neural tissues. The cleavage prediction based on human sequences had the best performance with a correct classification rate of cleaved and non-cleaved sites of 92% suggesting that the processing of prohormones in pigs is similar to humans. The cleavage prediction models did not find conclusive evidence supporting the production of the bioactive neuropeptides urocortin 2, urocortin 3, torsin family 2 member A, tachykinin 4, islet amyloid polypeptide, and calcitonin receptor-stimulating peptide 2 in the pig. Conclusions: The present genomic and functional characterization supports the use of the pig as an effective animal model to gain a deeper understanding of prohormones, prohormone convertases and neuropeptides in biomedical and agricultural research.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 6
    Publication Date: 2013-02-13
    Description: Motivation: Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of its impact on the accuracy of the enriched regions identified by peak-calling algorithms. Although many peak-calling algorithms include a fragment-length estimation subroutine, the problem has not been adequately solved, as demonstrated by the variability of the estimates returned by different algorithms. Results: In this article, we investigate the use of strand cross-correlation to estimate mean fragment length of single-end data and show that traditional estimation approaches have mixed reliability. We observe that the mappability of different parts of the genome can introduce an artificial bias into cross-correlation computations, resulting in incorrect fragment-length estimates. We propose a new approach, called mappability-sensitive cross-correlation (MaSC), which removes this bias and allows for accurate and reliable fragment-length estimation. We analyze the computational complexity of this approach, and evaluate its performance on a test suite of NGS datasets, demonstrating its superiority to traditional cross-correlation analysis. Availability: An open-source Perl implementation of our approach is available at http://www.perkinslab.ca/Software.html . Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 7
    Publication Date: 2013-02-06
    Description: Background: The current 'gold standard' for serotyping pneumococci is the Quellung test. This technique is laborious and requires a certain level of training to correctly perform. Commercial pneumococcal latex agglutination serotyping reagents are available, but these are expensive. In-house production of latex agglutination reagents can be a cost-effective alternative to using commercially available reagents. This paper describes a method for the production, and quality control (QC) of latex reagents, including problem solving recommendations, for pneumococcal serotyping. Results: Here we describe a method for the production of latex agglutination reagents based on the passive adsorption of antibodies to latex particles. Sixty-five latex agglutination reagents were made using the PneuCarriage Project (PCP) method, of which 35 passed QC. The other 30 reagents failed QC due to auto-agglutination (n=2), no reactivity with target serotypes (n=8) or cross-reactivity with non-target serotypes (n=20). Dilution of antisera resulted in a further 27 reagents passing QC. The remaining three reagents passed QC when prepared without centrifugation and wash steps. Protein estimates indicated that latex reagents that failed QC when prepared using the PCP method passed when made with antiserum containing
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 8
    Publication Date: 2012-04-25
    Description: The stability of RNAs bearing AU-rich elements in their 3'-UTRs, and thus the level of expression of their protein products, is regulated by interactions with cytoplasmic RNA-binding proteins. Binding by HuR generally leads to mRNA stabilization and increased protein production, whereas binding by AUF1 isoforms generally lead to rapid degradation of the mRNA and reduced protein production. The exact nature of the interplay between these and other RNA-binding proteins remains unclear, although recent studies have shown close interactions between them and even suggested competition between the two for binding to their cognate recognition sequences. Other recent reports have suggested that the sequences recognized by the two proteins are different. We therefore performed a detailed in vitro analysis of the binding site(s) for HuR and AUF1 present in androgen receptor mRNA to define their exact target sequences, and show that the same sequence is contacted by both proteins. Furthermore, we analysed a proposed HuR target within the 3'-UTR of MTA1 mRNA, and show that the contacted bases lie outside of the postulated motif and are a better match to a classical ARE than the postulated motif. The defining features of these HuR binding sites are their U-richness and single strandedness.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 9
    Publication Date: 2010-08-01
    Print ISSN: 0043-1354
    Electronic ISSN: 1879-2448
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Elsevier
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  • 10
    Publication Date: 2010-09-01
    Print ISSN: 0257-8972
    Electronic ISSN: 1879-3347
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Published by Elsevier
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