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Search Results: 1 - 10 of 438261 matches for " G?ran J?nsson "
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Estimating Coextinction Risks from Epidemic Tree Death: Affiliate Lichen Communities among Diseased Host Tree Populations of Fraxinus excelsior
Mari T. Jnsson, Gran Thor
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045701
Abstract: At least 10% of the world’s tree species are threatened with extinction and pathogens are increasingly implicated in tree threats. Coextinction and threats to affiliates as a consequence of the loss or decline of their host trees is a poorly understood phenomenon. Ash dieback is an emerging infectious disease causing severe dieback of common ash Fraxinus excelsior throughout Europe. We utilized available empirical data on affiliate epiphytic lichen diversity (174 species and 17,800 observations) among 20 ash dieback infected host tree populations of F. excelsior on the island Gotland in the Baltic Sea, Sweden. From this, we used structured scenario projections scaled with empirical data of ash dieback disease to generate probabilistic models for estimating local and regional lichen coextinction risks. Average coextinction probabilities (ā) were 0.38 (95% CI ±0.09) for lichens occurring on F. excelsior and 0.14 (95% CI ±0.03) when considering lichen persistence on all tree species. ā was strongly linked to local disease incidence levels and generally increasing with lichen host specificity to F. excelsior and decreasing population size. Coextinctions reduced affiliate community viability, with significant local reductions in species richness and shifts in lichen species composition. Affiliates were projected to become locally extirpated before their hosts, illuminating the need to also consider host tree declines. Traditionally managed open wooded meadows had the highest incidence of ash dieback disease and significantly higher proportions of affiliate species projected to go extinct, compared with unmanaged closed forests and semi-open grazed sites. Most cothreatened species were not previously red-listed, which suggest that tree epidemics cause many unforeseen threats to species. Our analysis shows that epidemic tree deaths represent an insidious, mostly overlooked, threat to sessile affiliate communities in forested environments. Current conservation and management strategies must account for secondary extinctions associated with epidemic tree death.
3D-bymodel over K benhavn - opbygning og anvendelse
Gran Jnsson,Niels Peter Jensen
Geoforum Perspektiv , 2004,
Calibration and assessment of channel-specific biases in microarray data with extended dynamical range
Henrik Bengtsson, Gran Jnsson, Johan Vallon-Christersson
BMC Bioinformatics , 2004, DOI: 10.1186/1471-2105-5-177
Abstract: By scanning the same spotted oligonucleotide microarray at different photomultiplier tube (PMT) gains, we have identified a channel-specific bias present in two-channel microarray data. For the scanners analyzed it was in the range of 15–25 (out of 65,535). The observed bias was very stable between subsequent scans of the same array although the PMT gain was greatly adjusted. This indicates that the bias does not originate from a step preceding the scanner detector parts. The bias varies slightly between arrays. When comparing estimates based on data from the same array, but from different scanners, we have found that different scanners introduce different amounts of bias. So do various image analysis methods. We propose a scanning protocol and a constrained affine model that allows us to identify and estimate the bias in each channel. Backward transformation removes the bias and brings the channels to the same scale. The result is that systematic effects such as intensity dependent log-ratios are removed, but also that signal densities become much more similar. The average scan, which has a larger dynamical range and greater signal-to-noise ratio than individual scans, can then be obtained.The study shows that microarray scanners may introduce a significant bias in each channel. Such biases have to be calibrated for, otherwise systematic effects such as intensity dependent log-ratios will be observed. The proposed scanning protocol and calibration method is simple to use and is useful for evaluating scanner biases or for obtaining calibrated measurements with extended dynamical range and better precision. The cross-platform R package aroma, which implements all described methods, is available for free from http://www.maths.lth.se/bioinformatics/ webcite.The microarray technology provides a way of simultaneously measuring transcript abundances of 103 – 105 genes from one or more cell or tissue samples. A microarray, also known as a gene chip, has well defined region
Health systems research in Lao PDR: capacity development for getting research into policy and practice
Kristina Jnsson, Gran Tomson, Christer Jnsson, Sengchanh Kounnavong, Rolf Wahlstr?m
Health Research Policy and Systems , 2007, DOI: 10.1186/1478-4505-5-11
Abstract: This article investigates the relationship between research and policymaking from the perspective of those participating in HSR projects. The study is based on 28 interviews, two group discussions and the responses from 56 questionnaires.The interviewees and questionnaire respondents were aware of the barriers to getting research into policy and practice. But while some were optimistic, claiming that there had been a change of attitudes among policymakers in the last two years, others were more pessimistic and did not expect any real changes until years from now. The major barriers to feeding research results into policy and practice included an inability to influence the policy process and to get policymakers and practitioners interested in research results. Another barrier was the lack of continuous capacity development and high-quality research, both of which are related to funding and international support. Many of the interviewees and questionnaire respondents also pointed out that communication between those conducting research and policymakers must be improved.The results show that in the case of Lao PDR, research capacity development is at a crucial stage for implementing research into policy and practice. If research is going to make a consistent impact on policymaking in the Lao health care sector, the attitude towards research will need to be changed in order to get research prioritised, both among those conducting research, and among policymakers and practitioners. Our findings indicate that there is awareness about the barriers in this process.This study seeks to contribute to the current discussion about health research feeding into policymaking in a low-income country setting. It is a follow-up of a previous article about research and policymaking in Lao PDR focusing on decision-makers and the usefulness of research evidence in policy implementation. It was concluded that health officials were very positive towards research, but that few seemed to ful
Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer
Johan Staaf, Gran Jnsson, Markus Ringnér, Bo Baldetorp, ?ke Borg
Breast Cancer Research , 2011, DOI: 10.1186/bcr3075
Abstract: High-density whole genome array-based comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) array data from 260 HER2-amplified breast tumors or cell lines, and 346 HER2-negative breast cancers with molecular subtype information were assembled from different repositories. Copy number alteration (CNA), loss-of-heterozygosity (LOH), copy number neutral allelic imbalance (CNN-AI), subclonal CNA and patterns of tumor DNA ploidy were analyzed using bioinformatical methods such as genomic identification of significant targets in cancer (GISTIC) and genome alteration print (GAP). The patterns of tumor ploidy were confirmed in 338 unrelated breast cancers analyzed by DNA flow cytometry with concurrent BAC aCGH and gene expression data.A core set of 36 genomic regions commonly affected by copy number gain or loss was identified by integrating results with a previous study, together comprising > 400 HER2-amplified tumors. While CNN-AI frequency appeared evenly distributed over chromosomes in HER2-amplified tumors, not targeting specific regions and often < 20% in frequency, the occurrence of LOH was strongly associated with regions of copy number loss. HER2-amplified and HER2-negative tumors stratified by molecular subtypes displayed different patterns of LOH and CNN-AI, with basal-like tumors showing highest frequencies followed by HER2-amplified and luminal B cases. Tumor aneuploidy was strongly associated with increasing levels of LOH, CNN-AI, CNAs and occurrence of subclonal copy number events, irrespective of subtype. Finally, SNP data from individual tumors indicated that genomic amplification in general appears as monoallelic, that is, it preferentially targets one parental chromosome in HER2-amplified tumors.We have delineated the genomic landscape of CNAs, amplifications, LOH, and CNN-AI in HER2-amplified breast cancer, but also demonstrated a strong association between different types of genomic aberrations and tumor aneuploidy irrespectiv
Normalization of array-CGH data: influence of copy number imbalances
Johan Staaf, Gran Jnsson, Markus Ringnér, Johan Vallon-Christersson
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-382
Abstract: Here we demonstrate that copy number imbalances correlate with intensity in array-CGH data thereby causing problems for conventional normalization methods. We propose a strategy to circumvent these problems by taking copy number imbalances into account during normalization, and we test the proposed strategy using several data sets from the analysis of cancer genomes. In addition, we show how the strategy can be applied to conveniently define adaptive sample-specific boundaries between balanced copy number, losses, and gains to facilitate management of variation in tissue heterogeneity when calling copy number changes.We highlight the importance of considering copy number imbalances during normalization of array-CGH data, and show how failure to do so can deleteriously affect data and hamper interpretation.Microarray-based techniques for genome-wide investigation of copy number aberrations (CNAs) have recently gained much attention. Initially employing arrays developed for gene expression analysis [1], or low-density arrays produced from large-insert genomic clones such as bacterial artificial chromosomes (BACs) [2], the application has evolved rapidly. Currently, specialized high-density arrays with oligonucleotide probes or probes derived from BAC clones are predominately used. Two-channel array-based comparative genomic hybridization (aCGH) is a direct successor to conventional metaphase CGH [3]. In both cases, DNA from two samples are differentially labeled with fluorescent dyes and co-hybridized to immobilized genomic capture probes. By use of aCGH, DNA derived from tumor tissue can be compared with reference DNA, e.g., normal whole blood DNA, and genomic imbalances can effectively be investigated. The main advantage of aCGH over conventional CGH is the increased resolution achieved by microarrays with a large number of individual probes, routinely up to hundreds of thousands, covering the entire genome [4]. The power of aCGH has been demonstrated in tumor studi
The Paris Declaration in practice: challenges of health sector aid coordination at the district level in Zambia
Jesper Sundewall, Birger C Forsberg, Kristina Jnsson, Collins Chansa, Gran Tomson
Health Research Policy and Systems , 2009, DOI: 10.1186/1478-4505-7-14
Abstract: The study was carried out in three districts of Zambia. Data were collected via interviews with health centre staff, district managers and officials from the Ministry of Health, and from district action plans, financial reports and accounts, and health centre ledger cards. Four indicators of coordination related to external-partner activity, common arrangements used by external partners and predictability of funding were analysed and assessed in relation to the 2010 targets set by the Paris Declaration.While the activity of external partners at the district level has increased, funding and activities provided by these partners are often not included in local plans. HIV/AIDS support show better integration in planning and implementation at the district level than other support. Regarding common arrangements used for fund disbursement, the share of resources provided as programme-based support is not increasing. The predictability of funds coming from outside the government financing mechanism is low.Greater efforts to integrate partners in district level planning and implementation are needed. External partners must improve the predictability of their support and be more proactive in informing the districts about their intended contributions. With the deadline for achieving the targets set by the Paris Declaration fast approaching, it is time for the signatories to accelerate its implementation.With increases in the number of donors and resources available, as well as the broadening diversity of aid projects in the past 20 years,[1,2] growing attention has been paid to optimizing the effectiveness of international aid, particularly in the health sector, and has highlighted the need for improvements in the coordination of donor efforts [3,4]. The Paris Declaration on Aid Effectiveness, endorsed in 2005, is an international agreement with 130 signatories (including more than 100 countries and organizations), which calls for increased harmonization, alignment and manage
Chest Wall Sarcoma: Outcome in 22 Patients After Resection Requiring Thoracic Cage Reconstruction
Per Jönsson,Erik Gyllstedt,Göran Hambraeus,Ramon Lillogil
Sarcoma , 1998, DOI: 10.1080/13577149877894
A case of Mycobacterium goodii prosthetic valve endocarditis in a non-immunocompromised patient: use of 16S rDNA analysis for rapid diagnosis
Jnsson Gran,Rydberg Johan,Stureg?rd Erik,Christensson Bertil
BMC Infectious Diseases , 2012, DOI: 10.1186/1471-2334-12-301
Abstract: Background Mycobacterium goodii is a rare cause of significant infection. M. goodii has mainly been associated with lymphadenitis, cellulitis, osteomyelitis, and wound infection. Case presentation A case of a 76-year-old Caucasian female is presented. The patient developed a prosthetic valve endocarditis caused by M. goodii. She had also suffered from severe neurological symptoms related to a septic emboli that could be demonstrated as an ischemic lesion found on CT of the brain. Transesophageal echocardiography verified a large vegetation attached to the prosthetic valve. Commonly used blood culture bottles showed growth of the bacteria after 3 days. Conclusions Although M. goodii is rarely involved in these kinds of severe infections, rapidly growing mycobacteria should be recognized during conventional bacterial investigations and identified by molecular tools such as analysis of 16S rDNA. Species identification of nontuberculous mycobacteria is demanding and is preferably done in collaboration with a mycobacterial laboratory. An early diagnosis provides the opportunity for adequate treatment. In the present case, prolonged antimicrobial treatment and surgery with replacement of the prosthetic valve was successful.
Tumor Genome Wide DNA Alterations Assessed by Array CGH in Patients with Poor and Excellent Survival Following Operation for Colorectal Cancer
Kristina K. Lagerstedt,Johan Staaf,Gran Jnsson,Elisabeth Hansson
Cancer Informatics , 2007,
Abstract: Genome wide DNA alterations were evaluated by array CGH in addition to RNA expression profiling in colorectal cancer from patients with excellent and poor survival following primary operations.DNA was used for CGH in BAC and cDNA arrays. Global RNA expression was determined by 44K arrays. DNA and RNA from tumor and normal colon were used from cancer patients grouped according to death, survival or Dukes A, B, C and D tumor stage. Confi rmed DNA alterations in all Dukes A – D were judged relevant for carcinogenesis, while changes in Dukes C and D only were regarded relevant for tumor progression.Copy number gain was more common than loss in tumor tissue (p 0.01). Major tumor DNA alterations occurred in chromosome 8, 13, 18 and 20, where short survival included gain in 8q and loss in 8p. Copy number gains related to tumor progression were most common on chromosome 7, 8, 19, 20, while corresponding major losses appeared in chromosome 8. Losses at chromosome 18 occurred in all Dukes stages. Normal colon tissue from cancer patients displayed gains in chromosome 19 and 20. Mathematical Vector analysis implied a number of BAC-clones in tumor DNA with genes of potential importance for death or survival. The genomic variation in colorectal cancer cells is tremendous and emphasizes that BAC array CGH is presently more powerful than available statistical models to discriminate DNA sequence information related to outcome. Present results suggest that a majority of DNA alterations observed in colorectal cancer are secondary to tumor progression. Therefore, it would require an immense work to distinguish primary from secondary DNA alterations behind colorectal cancer.
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