| 51. |
- Nelson, Ronald, et al.
(författare)
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qtl.outbred: Interfacing outbred line cross data with the R/qtl mapping software
- 2011
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Ingår i: BMC Research Notes. - : BioMed Central. - 1756-0500. ; 4:154
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Tidskriftsartikel (refereegranskat)abstract
- Backgroundqtl.outbred is an extendible interface in the statistical environment, R, for combining quantitative trait loci (QTL) mapping tools. It is built as an umbrella package that enables outbred genotype probabilities to be calculated and/or imported into the software package R/qtl.FindingsUsing qtl.outbred, the genotype probabilities from outbred line cross data can be calculated by interfacing with a new and efficient algorithm developed for analyzing arbitrarily large datasets (included in the package) or imported from other sources such as the web-based tool, GridQTL.Conclusionqtl.outbred will improve the speed for calculating probabilities and the ability to analyse large future datasets. This package enables the user to analyse outbred line cross data accurately, but with similar effort than inbred line cross data.
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| 52. |
- Nerpin, Elisabet, et al.
(författare)
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Inflammation, oxidative stress, glomerular filtration rate, and albuminuria in elderly men : a cross-sectional study
- 2012
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Ingår i: BMC research notes. - : BioMed Central. - 1756-0500. ; 5:1, s. 537-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The role of inflammation and oxidative stress in mild renal impairment in the elderly is not well studied. Accordingly, we aimed at investigating the associations between estimated glomerular filtration rate (eGFR), albumin/creatinine ratio (ACR), and markers of different inflammatory pathways and oxidative stress in a community based cohort of elderly men. FINDINGS: Cystatin C-based GFR, ACR, and biomarkers of cytokine-mediated inflammation (interleukin-6, high-sensitivity C-reactive protein[CRP], serum amyloid A[SAA]), cyclooxygenase-mediated inflammation (urinary prostaglandin F2alpha [PGF2alpha]), and oxidative stress (urinary F2 isoprostanes) were assessed in the Uppsala Longitudinal Study of Adult Men(n = 647, mean age 77 years). RESULTS: In linear regression models adjusting for age, BMI, smoking, blood pressure, LDL-cholesterol, HDL-cholesterol, triglycerides, and treatment with statins, ACE-inhibitors, ASA, and anti-inflammatory agents, eGFR was inversely associated with CRP, interleukin-6, and SAA (beta-coefficient -0.13 to -0.19, p < 0.001 for all), and positively associated with urinary F2-isoprostanes (beta-coefficient 0.09, p = 0.02). In line with this, ACR was positively associated with CRP, interleukin-6, and SAA (beta- coefficient 0.09-0.12, p < 0.02 for all), and negatively associated with urinary F2-isoprostanes (beta-coefficient -0.12, p = 0.002). The associations were similar but with lower regression coefficients in a sub-sample with normal eGFR (>60 ml/min/1.73 m2, n = 514), with the exception that F2-isoprostane and SAA were no longer associated with eGFR. CONCLUSION: Our data indicate that cytokine-mediated inflammation is involved in the early stages of impaired kidney function in the elderly, but that cyclooxygenase-mediated inflammation does not play a role at this stage. The unexpected association between higher eGFR/lower albuminuria and increased F2-isoprostanes in urine merits further studies.
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| 53. |
- Olsson, Lovisa A., 1950-, et al.
(författare)
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Renal function is a determinant of subjective well-being in active seniors but not in patients with subjective memory complaints
- 2014
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 7, s. 647-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: During our whole life span, factors influencing health and functioning are accumulated. In chronic kidney disease, quality of life is adversely affected. We hypothesized that biomarkers of renal function could also be determinants of subjective well-being (SWB) in Swedish elderly subjects. SWB was assessed by the Psychological General Well-Being index (PGWB index) in two study groups: Active seniors (AS) consisted of community-dwelling elderly Swedes leading an active life (n = 389), and the DGM cohort (n = 300) consisted of subjects referred to the Memory Unit at the Department of Geriatrics for memory problems, Serum creatinine, cystatin C, and eGFR (CKD-EPI) were used as biomarkers of renal function.RESULTS: There were no significant differences in cystatin C and eGFR values between the two cohorts: cystatin C medians 0.88 vs 0.86 mg/L and eGFR 73 vs 80 mL/min/1.73 m2 (AS vs DGM). In the AS cohort cystatin C was negatively related to PGWB index in women (P < 0.001, R2 ≈ 5%), and the covariates age and BMI did not improve the models. The renal biomarkers were unrelated to the PGWB index in the DGM cohort. Cystatin C in the AS cohort was adversely related to the PGWB subdimensions anxiety, depressed mood, positive well-being, and vitality in women, but in men only to depressed mood (P < 0.006; R2 ≈ 6%). In the DGM cohort, depressed mood in men was also significantly related to cystatin C (P = 0.050), but not in women.CONCLUSIONS: Renal function even within the normal range, measured by serum cystatin C concentration, has significant and sex specific associations with subjective well-being and its subdimensions in healthy elderly subjects. Maintenance of good renal function in aging may be of importance in maintaining a high subjective well-being.
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| 54. |
- Papp, Marian E, et al.
(författare)
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Increased heart rate variability but no effect on blood pressure from 8 weeks of hatha yoga - a pilot study
- 2013
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 6:59, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundYoga exercises are known to decrease stress and restore autonomic balance. Yet knowledge about the physiological effects of inversion postures is limited. This study aimed to investigate the effects of inversion postures (head below the heart) on blood pressure (BP) and heart rate variability (HRV).MethodsTwelve healthy women and men took part in an 8-week yoga program (60 min once a week). BP was measured with an automatic Omron mx3 oscillometric monitoring device and HRV with a Holter 24-hour ECG at baseline and 8 weeks after the intervention.ResultsThere was no significant effect of inversion postures on BP. Nine out of 12 participants showed a significant increase in HRV (p < 0.05) at night (2 hours) on pNN50% (12.7 +/- 12.5 to 18.2 +/- 13.3). There were no significant changes in other HRV measures such as NN50, LF, HF, LF/HF ratio, LF normalized units (n.u.), HF n.u. and RMSSD.ConclusionEight weeks of hatha yoga improved HRV significantly which suggests an increased vagal tone and reduced sympathetic activity.
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| 55. |
- Pedersen, Kristina, et al.
(författare)
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A simple way to evaluate self-designed probes for tumor specific Multiplex Ligation-dependent Probe Amplification (MLPA)
- 2010
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Ingår i: BMC Research Notes. - : BioMed Central Ltd. - 1756-0500. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:The Multiplex Ligation-dependent Probe Amplification (MLPA) is widely used for analysis of copy number variations (CNVs) in single or multiple loci. MLPA is a versatile methodology and important tool in cancer research; it provides precise information on increased or decreased copy number at specific loci as opposed to loss of heterozygosity (LOH) studies based upon microsatellite analysis. Pre-designed MLPA kits and software are commercially available to analyze multiple exons, genes, and genomic regions. However, an increasing demand for new gene specific assays makes it necessary to self-design new MLPA probes for which the available software may not be applicable. During evaluation of new self-designed reference probes, we encountered a number of problems, especially when applying the MLPA methodology to tumor samples.FINDINGS:DNA samples from 48 unaffected individuals and 145 breast cancer patients were used to evaluate 11 self-designed MLPA probes and determine the cut-off values for CNV, before applying the MLPA probes to normalize the target probes in a cohort of affected individuals. To test the calculation strategy, three probes were designed to cover regions in Regulator of G-protein Signaling 8 (RGS8), which we previously have identified as being affected by allelic imbalance by LOH analysis across RGS8 in the cohort comprising 145 breast tumors. Agreement between the LOH results and the results obtained by each of the three MLPA probes in RGS8 was found for 64%, 73%, and 91%, of the analyzed samples, respectively.CONCLUSION:Here, we present a straightforward method, based upon the normalization pattern in both unaffected and affected individuals, to evaluate self-designed reference probes and to calculate CNV for the MLPA assay with specific focus on the difficulties when analyzing tumor DNA.
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| 56. |
- Pettersson, Ann, et al.
(författare)
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Chromogranins can be measured in samples from cats and dogs
- 2014
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Background: Methods for objective evaluation of stress in animals are important, but clinically difficult. An alternative method to study the sympathetic activity may be to investigate Chromogranin A (CGA), Chromogranin B (CGB) and Secretogranin II (SG2). The aim of this study was to investigate the cross-reactivity of CGA, CGB and SG2 between man, cat and dog and to explore possibilities to measure these proteins in samples from cats and dogs. Results: Adrenal gland extracts from feline and canine species were measured by region-specific radioimmunoassays in different dilution steps to explore possible inter species cross reactivity. High cross reactivity was found for cats in the CGA17-38, CGA324-337, CGA361-372, CGB and SG2 assays. High cross reactivity was found for dogs in the CGA17-38, CGA361-372, CGB and SN assays. The method measuring the intact CGA was not useful for measurements in cats and dogs. Conclusions: Region-specific assays measuring defined parts of CGA, CGB and SG2 can be used for measurements in samples from cats and dogs. These results are promising and will allow for further studies of these proteins as possible clinical biomarkers in cats and dogs. Keywords: Chromogranin, Secretogranin, Canine, Feline, Human, Radioimmunoassay
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| 57. |
- Prieto-Velasco, Mario, et al.
(författare)
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Predialysis education in practice : a questionnaire survey of centres with established programmes.
- 2014
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Ingår i: BMC research notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 7, s. 730-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: There is growing evidence that renal replacement therapy option education (RRTOE) can result in enhanced quality of life, improved clinical outcomes, and reduced health care costs. However, there is still no detailed guidance on the optimal way to run such programmes. To help address this knowledge gap, an expert meeting was held in March 2013 to formulate a position statement on optimal ways to run RRTOE. Experts were selected from units that had extensive experience in RRTOE or were performing research in this field. Before the meeting, experts completed a pilot questionnaire on RRTOE in their own units. They also prepared feedback on how to modify this questionnaire for a large-scale study.METHODS: A pilot, web-based questionnaire was used to obtain information on: the renal unit and patients, the education team, RRTOE processes and content, how quality is assessed, and funding.RESULTS: Four nurses, 5 nephrologists and 1 clinical psychologist (9 renal units; 6 EU countries) participated. Nurses were almost always responsible for organising RRTOE. Nephrologists spent 7.5% (median) of their time on RRTOE. Education for the patient and family began several months before dialysis or according to disease progression. Key topics such as the 'impact of the disease' were covered by every unit, but only a few units described all dialysis modalities. Visits to the unit were almost always arranged. Materials came in a wide variety of forms and from a wide range of sources. Group education sessions were used in 3/9 centres. Expectations on the timing of patients' decisions on modality and permanent access differed substantially between centres. Common quality assurance measures were: patient satisfaction, course attendance, updated materials. Only 1 unit had a dedicated budget.CONCLUSIONS: There were substantial variations in how RRTOE is run between the units. A modified version of this questionnaire will be used to assess RRTOE at a European level.
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| 58. |
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| 59. |
- Riise, Gerdt C., 1956, et al.
(författare)
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Prediction of BOS by the single-breath nitrogen test in double lung transplant recipients.
- 2011
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Ingår i: BMC research notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The present study analyses the ability of the alveolar slope of the single-breath nitrogen washout test (N2-slope) to diagnose and predict the development of the bronchiolitis obliterans syndrome (BOS). METHODS: We present a retrospective analysis of 61 consecutive bilateral lung or heart-lung transplant recipients who were followed at regular control visits during a three year follow-up. The operating characteristics of the N2-slope to diagnose BOS and potential BOS (BOS 0-p) and to predict BOS were determined based on cut off values of 95% specificity. RESULTS: The sensitivity of the N2-slope to identify BOS was 96%, and BOS 0-p 100%. The predictive ability to predict BOS with a N2-slope > 478% of the predicted normal was 56%, and if combined with a coincident FEV1 < 90% of the basal value, the predictive ability was 75%. CONCLUSIONS: The predictive ability of either the N2-slope or of FEV1 to diagnose BOS is limited but the combination of the two appears useful. Follow-up protocols of bilateral lung and heart-lung transplant recipients should consider including tests sensitive to obstruction of the peripheral airways.
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| 60. |
- Rincon, Gonzalo, et al.
(författare)
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Comparison of buccal and blood-derived canine DNA, either native or whole genome amplified, for array-based genome-wide association studies
- 2011
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4, s. 226-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:The availability of array-based genotyping platforms for single nucleotide polymorphisms (SNPs) for the canine genome has expanded the opportunities to undertake genome-wide association (GWA) studies to identify the genetic basis for Mendelian and complex traits. Whole blood as the source of high quality DNA is undisputed but often proves impractical for collection of the large numbers of samples necessary to discover the loci underlying complex traits. Further, many countries prohibit the collection of blood from dogs unless medically necessary thereby restricting access to critical control samples from healthy dogs. Alternate sources of DNA, typically from buccal cytobrush extractions, while convenient, have been suggested to have low yield and perform poorly in GWA. Yet buccal cytobrushes provide a cost-effective means of collecting DNA, are readily accepted by dog owners, and represent a large resource base in many canine genetics laboratories. To increase the DNA quantities, whole genome amplification (WGA) can be performed. Thus, the present study assessed the utility of buccal-derived DNA as well as whole genome amplification in comparison to blood samples for use on the most recent iteration of the canine HD SNP array (Illumina).FINDINGS:In both buccal and blood samples, whether whole genome amplified or not, 97% of the samples had SNP call rates in excess of 80% indicating that the vast majority of the SNPs would be suitable to perform association studies regardless of the DNA source. Similarly, there were no significant differences in marker intensity measurements between buccal and blood samples for copy number variations (CNV) analysis.CONCLUSIONS:All DNA samples assayed, buccal or blood, native or whole genome amplified, are appropriate for use in array-based genome-wide association studies. The concordance between subsets of dogs for which both buccal and blood samples, or those samples whole genome amplified, was shown to average >99%. Thus, the two DNA sources were comparable in the generation of SNP genotypes and intensity values to estimate structural variation indicating the utility for the use of buccal cytobrush samples and the reliability of whole genome amplification for genome-wide association and CNV studies.
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