| 11. |
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| 12. |
- Malm, Johan, et al.
(författare)
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Developments in biobanking workflow standardization providing sample integrity and stability
- 2013
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 95:SI, s. 38-45
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Tidskriftsartikel (refereegranskat)abstract
- Recommendations and outlines for standardization in biobanking processes are presented by a research team with long-term experience in clinical studies. These processes have important bearing on the use of samples in developing assays. These measurements are useful to document states of health and disease that are beneficial for academic research, commercial healthcare, drug development industry and government regulating agencies. There is a need for increasing awareness within proteomic and genomic communities regarding the basic concepts of collecting, storing and utilizing clinical samples. Quality control and sample suitability for analysis need to be documented and validated to ensure data integrity and establish contexts for interpretation of results. Standardized methods in proteomics and genomics are required to be practiced throughout the community allowing datasets to be comparable and shared for analysis. For example, sample processing of thousands of clinical samples, performed in 384 high-density sample tube systems in a fully automated workflow, preserves sample content and is presented showing validation criteria. Large studies will be accompanied by biological and molecular information with corresponding clinical records from patients and healthy donors. These developments position biobanks of human patient samples as an increasingly recognized major asset in disease research, future drug development and within patient care. Biological significance: The current manuscript is of major relevance to the proteomic and genomic fields, as it outlines the standardization aspects of biobanking and the requirements that are needed to run future clinical studies that will benefit the patients where OMICS science will play a major role. A global view of the field is given where best practice and conventional acceptances are presented along with ongoing large-scale biobanking projects. The authors represent broadly stakeholders that cover the academic, pharma, biotech and healthcare fields with extensive experience and deliveries. This contribution will be a milestone paper to the proteomic and genomic scientists to present data in the future that will have impact to the life science area.This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.
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| 13. |
- Nilsson, C. L., et al.
(författare)
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Chromosome 19 Annotations with Disease Speciation: A First Report from the Global Research Consortium
- 2013
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 12:1, s. 134-149
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Tidskriftsartikel (refereegranskat)abstract
- A first research development progress report of the Chromosome 19 Consortium with members from Sweden, Norway, Spain, United States, China and India, a part of the Chromosome-centric Human Proteome Project (C-HPP) global initiative, is presented (http://www.c-hpp.org). From the chromosome 19 peptide-targeted library constituting 6159 peptides, a pilot study was conducted using a subset with 125 isotope-labeled peptides. We applied an annotation strategy with triple quadrupole, ESI-Qtrap, and MALDI mass spectrometry platforms, comparing the quality of data within and in between these instrumental set-ups. LC–MS conditions were outlined by multiplex assay developments, followed by MRM assay developments. SRM was applied to biobank samples, quantifying kallikrein 3 (prostate specific antigen) in plasma from prostate cancer patients. The antibody production has been initiated for more than 1200 genes from the entire chromosome 19, and the progress developments are presented. We developed a dedicated transcript microarray to serve as the mRNA identifier by screening cancer cell lines. NAPPA protein arrays were built to align with the transcript data with the Chromosome 19 NAPPA chip, dedicated to 90 proteins, as the first development delivery. We have introduced an IT-infrastructure utilizing a LIMS system that serves as the key interface for the research teams to share and explore data generated within the project. The cross-site data repository will form the basis for sample processing, including biological samples as well as patient samples from national Biobanks.
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| 14. |
- Végvári, Ákos, et al.
(författare)
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Essential tactics of tissue preparation and matrix nano-spotting for successful compound imaging mass spectrometry
- 2010
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1876-7737 .- 1874-3919. ; 73:6, s. 1270-1278
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Tidskriftsartikel (refereegranskat)abstract
- The ultimate goal of MALDI-Imaging Mass Spectrometry (MALDI-IMS) is to achieve spatial localization of analytes in tissue sections down to individual tissue compartments or even at the level of a few cells. With compound tissue imaging, it is possible to track the transportation of an unlabelled, inhaled reference compound within lung tissue, through the application of MALDI-IMS. The procedure for isolation and preparation of lung tissues is found to be crucial in order to preserve the anatomy and structure of the pulmonary compartments. To avoid delocalization of analytes within lung tissue compartments we have applied an in-house designed nano-spotter, based on a microdispenser mounted on an XY table, of which movement and spotting functionality were fully computer controlled. We demonstrate the usefulness of this platform in lung tissue sections isolated from rodent in vivo model, applied to compound tissue imaging as exemplified with the determination of the spatial distribution of (1 alpha,2 beta,4 beta,7 beta)-7-[(hydroxidi-2-thienylacetyl)oxy]-9,9-dimethyl-3-oxa-9-azoniatric yclo[3.3.1.0(2,4)]nonane, also known as tiotropium. We provide details on tissue preparation protocols and sample spotting technology for successful identification of drug in mouse lung tissue by using MALDI-Orbitrap instrumentation.
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| 15. |
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| 16. |
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| 17. |
- Andrén, Olof, et al.
(författare)
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Carbon balances in US croplands during the last two decades of the twentieth century
- 2012
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Ingår i: Biogeochemistry. - : Springer Science and Business Media LLC. - 0168-2563 .- 1573-515X. ; 107, s. 207-225
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Tidskriftsartikel (refereegranskat)abstract
- Carbon (C) added to soil as organic matter in crop residues and carbon emitted to the atmosphere as CO(2) in soil respiration are key determinants of the C balance in cropland ecosystems. We used complete and comprehensive county-level yields and area data to estimate and analyze the spatial and temporal variability of regional and national scale residue C inputs, net primary productivity (NPP), and C stocks in US croplands from 1982 to 1997. Annual residue C inputs were highest in the North Central and Central and Northern Plains regions that comprise similar to 70% of US cropland. Average residue C inputs ranged from 1.8 (Delta States) to 3.0 (North Central region) Mg C ha(-1) year(-1), and average NPP ranged from 3.1 (Delta States) to 5.4 (Far West region) Mg C ha(-1) year(-1). Residue C inputs tended to be inversely proportional to the mean growing season temperature. A quadratic relationship incorporating the growing season mean temperature and total precipitation closely predicted the variation in residue C inputs in the North Central region and Central and Northern Plains. We analyzed the soil C balance using the crop residue database and the Introductory Carbon Balance regional Model (ICBMr). Soil C stocks (0-20 cm) on permanent cropland ranged between 3.07 and 3.1 Pg during the study period, with an average increase of similar to 4 Tg C year(-1), during the 1990s. Interannual variability in soil C stocks ranged from 0 to 20 Tg C (across a mean C stock of 3.08 +/- A 0.01 Pg) during the study period; interannual variability in residue C inputs varied between 1 and 43 Tg C (across a mean input of 220 +/- A 19 Tg). Such interannual variation has implications for national estimates of CO(2) emissions from cropland soils needed for implementation of greenhouse gas (GHG) mitigation strategies involving agriculture.
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| 18. |
- Andrén, Olof, et al.
(författare)
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How can soil monitoring networks be used to improve predictions of organic carbon pool dynamics and CO2 fluxes in agricultural soils?
- 2011
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Ingår i: Plant and Soil. - : Springer Science and Business Media LLC. - 0032-079X .- 1573-5036. ; 338, s. 247-259
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Tidskriftsartikel (refereegranskat)abstract
- As regional and continental carbon balances of terrestrial ecosystems become available, it becomes clear that the soils are the largest source of uncertainty. Repeated inventories of soil organic carbon (SOC) organized in soil monitoring networks (SMN) are being implemented in a number of countries. This paper reviews the concepts and design of SMNs in ten countries, and discusses the contribution of such networks to reducing the uncertainty of soil carbon balances. Some SMNs are designed to estimate country-specific land use or management effects on SOC stocks, while others collect soil carbon and ancillary data to provide a nationally consistent assessment of soil carbon condition across the major land-use/soil type combinations. The former use a single sampling campaign of paired sites, while for the latter both systematic (usually grid based) and stratified repeated sampling campaigns (5-10 years interval) are used with densities of one site per 10-1,040 kmA(2). For paired sites, multiple samples at each site are taken in order to allow statistical analysis, while for the single sites, composite samples are taken. In both cases, fixed depth increments together with samples for bulk density and stone content are recommended. Samples should be archived to allow for re-measurement purposes using updated techniques. Information on land management, and where possible, land use history should be systematically recorded for each site. A case study of the agricultural frontier in Brazil is presented in which land use effect factors are calculated in order to quantify the CO2 fluxes from national land use/management conversion matrices. Process-based SOC models can be run for the individual points of the SMN, provided detailed land management records are available. These studies are still rare, as most SMNs have been implemented recently or are in progress. Examples from the USA and Belgium show that uncertainties in SOC change range from 1.6-6.5 Mg C ha(-1) for the prediction of SOC stock changes on individual sites to 11.72 Mg C ha(-1) or 34% of the median SOC change for soil/land use/climate units. For national SOC monitoring, stratified sampling sites appears to be the most straightforward attribution of SOC values to units with similar soil/land use/climate conditions (i.e. a spatially implicit upscaling approach).
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| 19. |
- Andrén, Peter, 1972-, et al.
(författare)
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Prognosmodeller för tillståndsmått i Trafikverkets Pavement Management System : IRI och spårdjup
- 2014
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Vägytans tillstånd på det statliga svenska vägnätet har inventerats med mätbil sedan 1987. Av kostnadsskäl mäts inte alla vägar varje år, istället kan man använda modeller som prognostiserar tillståndet för de år då mätningar saknas. Syftet med vägytemätningarna är att förse Trafikverkets Pavement Management System (PMS) med tillståndsdata. De främsta användningsområdena för tillståndsmåtten är: • Beskrivning av det övergripande vägtillståndet och tillståndförändringen för att bedöma hur valda drift- och underhållsstrategier lyckats. • Stöd vid underhållsplanering. • Underlag vid beräkning av framtida underhållsbehov. • Stöd vid val av åtgärdsmetod. • Kontroll av utförande av byggnation eller underhåll. • Stöd vid forskning. Trafikverket har behov av en fullständig tillståndsbeskrivning av vägnätet, bland annat för att kunna redovisa för regering och riksdag hur uppdraget att underhålla statens vägar fullföljs. Ett sätt att årligen beskriva tillståndet för hela vägnätet är att använda modeller som prognostiserar tillståndet för de år då mätningar saknas. I valet mellan att använda en global eller lokal modell för att beskriva tillståndsutvecklingen för IRI (International Roughness Index) och spårdjup på enskilda 100-meterssegment visar rapporten att en modell med lokal anpassning är att föredra. Vid anpassning av en global modell får forskarna inte tillräckligt hög förklaringsgrad och ser inte heller ett konsekvent mönster i regressionskoefficienterna för de förklaringsvariabler som provats.
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| 20. |
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