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1.
  • Aaltonen, Kristina, et al. (författare)
  • Laser capture microdissection (LCM) and whole genome amplification (WGA) of DNA from normal breast tissue - optimization for genome wide array analyses.
  • 2011
  • Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4, s. 69-69
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Laser capture microdissection (LCM) can be applied to tissues where cells of interest are distinguishable from surrounding cell populations. Here, we have optimized LCM for fresh frozen normal breast tissue where large amounts of fat can cause problems during microdissection. Since the amount of DNA needed for genome wide analyses, such as single nucleotide polymorphism (SNP) arrays, is often greater than what can be obtained from the dissected tissue, we have compared three different whole genome amplification (WGA) kits for amplification of DNA from LCM material. In addition, the genome wide profiling methods commonly used today require extremely high DNA quality compared to PCR based techniques and DNA quality is thus critical for successful downstream analyses. Findings We found that by using FrameSlides without glass backing for LCM and treating the slides with acetone after staining, the problems caused by excessive fat could be significantly decreased. The amount of DNA obtained after extraction from LCM tissue was not sufficient for direct SNP array analysis in our material. However, the two WGA kits based on Phi29 polymerase technology (Repli-g® (Qiagen) and GenomiPhi (GE Healthcare)) gave relatively long amplification products, and amplified DNA from Repli-g® gave call rates in the subsequent SNP analysis close to those from non-amplified DNA. Furthermore, the quality of the input DNA for WGA was found to be essential for successful SNP array results and initial DNA fragmentation problems could be reduced by switching from a regular halogen lamp to a VIS-LED lamp during LCM. Conclusions LCM must be optimized to work satisfactorily in difficult tissues. We describe a work flow for fresh frozen normal breast tissue where fat is inclined to cause problems if sample treatment is not adapted to this tissue. We also show that the Phi29-based Repli-g® WGA kit (Qiagen) is a feasible approach to amplify DNA of high quality prior to genome wide analyses such as SNP profiling.
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2.
  • Hedman, Johannes, et al. (författare)
  • A ranking index for quality assessment of forensic DNA profiles
  • 2010
  • Ingår i: BMC Research Notes. - : BioMed Central Ltd. - 1756-0500. ; 3:290
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundAssessment of DNA profile quality is vital in forensic DNA analysis, both in order to determine the evidentiary value of DNA results and to compare the performance of different DNA analysis protocols. Generally the quality assessment is performed through manual examination of the DNA profiles based on empirical knowledge, or by comparing the intensities (allelic peak heights) of the capillary electrophoresis electropherograms.ResultsWe recently developed a ranking index for unbiased and quantitative quality assessment of forensic DNA profiles, the forensic DNA profile index (FI) (Hedman et al. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles, Biotechniques 47 (2009) 951-958). FI uses electropherogram data to combine the intensities of the allelic peaks with the balances within and between loci, using Principal Components Analysis. Here we present the construction of FI. We explain the mathematical and statistical methodologies used and present details about the applied data reduction method. Thereby we show how to adapt the ranking index for any Short Tandem Repeat-based forensic DNA typing system through validation against a manual grading scale and calibration against a specific set of DNA profiles.ConclusionsThe developed tool provides unbiased quality assessment of forensic DNA profiles. It can be applied for any DNA profiling system based on Short Tandem Repeat markers. Apart from crime related DNA analysis, FI can therefore be used as a quality tool in paternal or familial testing as well as in disaster victim identification.
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3.
  • Freyhult, Eva, et al. (författare)
  • Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update
  • 2008
  • Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 1:49, s. 1-8
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundThe H/ACA family of small nucleolar RNAs (snoRNAs) plays a central role in guiding the pseudouridylation of ribosomal RNA (rRNA). In an effort to systematically identify the complete set of rRNA-modifying H/ACA snoRNAs from the genome sequence of the budding yeast, Saccharomyces cerevisiae, we developed a program - Fisher - and previously presented several candidate snoRNAs based on our analysis [1]. FindingsIn this report, we provide a brief update of this work, which was aborted after the publication of experimentally-identified snoRNAs [2] identical to candidates we had identified bioinformatically using Fisher. Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in [1], and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program [3]. While we are no longer developing Fisher, we briefly consider the merits of the Fisher algorithm relative to snoGPS, which may be of use for workers considering pursuing a similar search strategy for the identification of small RNAs. The modified source code for Fisher is made available as supplementary material. ConclusionOur results confirm the validity of using minimum free energy (MFE) secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints. 
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4.
  • Willighagen, Egon, et al. (författare)
  • Computational toxicology using the OpenTox application programming interface and Bioclipse
  • 2011
  • Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4:1, s. 487-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. Findings: This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. Conclusions: A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers.
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5.
  • Andriesse, Hanneke, et al. (författare)
  • Reliability and validity of motion analysis in children treated for congenital clubfoot according to the Clubfoot Assessment Protocol (CAP) using inexperienced assessors
  • 2009
  • Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 2
  • Tidskriftsartikel (refereegranskat)abstract
    • Background. The Clubfoot Assessment Protocol (CAP) was developed for follow-up of children treated for clubfoot. The objective of this study was to analyze reliability and validity of the six items used in the domain CAPMotion Quality using inexperienced assessors. Findings. Four raters (two paediatric orthopaedic surgeons, two senior physiotherapists) used the CAP scores to analyze, on two different occasions, 11 videotapes containing standardized recordings of motion activity according to the domain CAPMotion Quality These results were compared to a criterion (two raters, well experienced CAP assessors) for validity and for checking for learning effect. Weighted kappa statistics, exact percentage observer agreement (Po), percentage observer agreement including one level difference (Po-1) and amount of scoring scales defined how reliability was to be interpreted. Inter- and intra rater differences were calculated using median and inter quartile ranges (IQR) on item level and mean and limits of agreement on domain level. Inter-rater reliability varied between fair and moderate (kappa) and had a mean agreement of 48/88% (Po/Po-1). Intra -rater reliability varied between moderate to good with a mean agreement of 63/96%. The intra- and inter-rater differences in the present study were generally small both on item (0.00) and domain level (-1.10). There was exact agreement of 51% and Po-1 of 91% of the six items with the criterion. No learning effect was found. Conclusion. The CAPMotion quality can be used by inexperienced assessors with sufficient reliability in daily clinical practice and showed acceptable accuracy compared to the criterion.
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6.
  • Arenaz Bua, Beatriz, et al. (författare)
  • Validation in Swedish of sydney swallow questionnaire.
  • 2014
  • Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 7:1
  • Tidskriftsartikel (refereegranskat)abstract
    • The aim of this study was to translate and adapt the Sydney Swallow Questionnaire to Swedish conditions and to evaluate the validity and test-retest reliability of the Swedish translation in patients with oropharyngeal dysphagia and in healthy controls.
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7.
  • Benamer, Hani Ts, et al. (författare)
  • The Libyan doctors' brain drain: an exploratory study.
  • 2009
  • Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 2:Dec 8
  • Tidskriftsartikel (refereegranskat)abstract
    • ABSTRACT: BACKGROUND: Medical emigration from developing to developed countries is a well established phenomenon of substantial importance. Though Libya is classified as an upper-middle income country, it has been affected by this trend. This study was undertaken to identify some of the possible reasons behind the emigration of Libyan doctors and factors that might motivate them to return. FINDINGS: Seventy-four completed questionnaires were analysed. Median age of the respondents was 43 years (33-60) and median duration of stay outside Libya was 15 years (6-29). Most of the participants were resident in Europe (66%). The desire to further their education and research was the main reason given by 88% of the respondents for leaving Libya, while 50% of them gave that as the main reason for staying abroad. One-third of the respondents (31%) cited economic factors as the main reason for not returning. None of the respondents ruled out returning to Libya, and about half of them stated that they definitely or probably will return to Libya. 58% ranked reform of the Libyan health system as the most important reason that could induce them to return to Libya. CONCLUSION: The study shows that reforming the health care system in Libya might induce some of the physicians who moved abroad mainly for educational and economic reasons to return to Libya to practice medicine.
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8.
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9.
  • Biru, Mulatu, et al. (författare)
  • Prophylactic treatment uptake and compliance with recommended follow up among HIV exposed infants : a retrospective study in Addis Ababa, Ethiopia
  • 2011
  • Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4, s. 563-563
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Children are being infected by HIV/AIDS mainly through mother-to-child transmission. In Ethiopia currently more than 135,000 children are living with HIV/AIDS. The aim of this study was to describe the pattern of ARV uptake after birth, co-trimoxazole prophylaxis and follow up compliance, and to examine which factors are associated with the intervention outcome.METHODS: A retrospective quantitative study design was used for data collection through two hospitals. All infants who were delivered by HIV infected mothers between October 2008 and August 2009 were included and information regarding treatment adherence during their first 6 months of age was collected.FINDINGS: 118 HIV exposed infant-mother pairs were included in the study. 107 (90.7%) infants received ARV prophylaxis at birth. Sixty six (56%) of the infants were found to be adherent to co-trimoxazole prophylactic treatment. The majority (n = 110(93.2%)) of infants were tested HIV negative with DNA/PCR HIV test at the age of sixth weeks. Infants who took ARV prophylaxis at birth were found to be more likely to adhere with co-trimoxazole treatment: [OR = 9.43(95% CI: 1.22, 72.9)]. Similarly, infants whose mothers had been enrolled for HIV/ART care in the same facility [OR = 14(95% CI: 2.6, 75.4)], and children whose fathers were tested and known to be HIV positive [OR = 3.0(95% CI: 1.0, 9.0)] were more likely to adhere than their counterparts. Infants feeding practice was also significantly associated with adherence χ2 -test, p < 0.01.CONCLUSION: The proportion of ARV uptake at birth among HIV exposed infants were found to be high compared to other similar settings. Mother-infant pair enrolment in the same facility and the infant's father being tested and knew their HIV result were major predictors of infants adhering to treatment and follow up. However, large numbers of infants were lost to follow up.
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10.
  • Borg, Julia, et al. (författare)
  • Oxytocin prolongs the gastric emptying time in patients with diabetes mellitus and gastroparesis, but does not affect satiety or volume intake in patients with functional dyspepsia
  • 2012
  • Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Oxytocin is released in response to a fatty meal. Blockage of the oxytocin receptor led to slower gastric emptying whereas stimulation resulted in less satiety in healthy volunteers. Patients with diabetes mellitus and gastroparesis lack oxytocin elevation, and dyspepsia is partly caused by reduced fundus accommodation causing early satiety and related symptoms. The aim of this study was thus to examine the effect of oxytocin on gastric emptying, satiety and volume intake in patients with gastrointestinal pathology. Results: Gastric emptying scintigraphy was performed twice in 12 patients with diabetic gastroparesis, once with oxytocin and once with saline as intravenous infusions. The patients scored their sensation of satiety using a visual analogue scale (VAS). The gastric emptying in patients with gastroparesis was prolonged during oxytocin infusion (p = 0.034) without affecting satiety. A slow satiety drinking test was performed in 14 patients with functional dyspepsia. The patients scored their satiety every five minutes until maximal satiety was reached, and the total volume was determined. The VAS was also completed 30 minutes afterwards. The test was performed twice, once with oxytocin and once with saline as intravenous infusions. There was no difference in satiety scores or volume of nutrient intake between saline and oxytocin infusions, either before, during or after the meal. Conclusions: Oxytocin prolongs gastric emptying in patients with diabetes mellitus and gastroparesis, but has no effect on volume of nutrient intake or satiety and other related symptoms in patients with functional dyspepsia.
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