1. |
- Aaltonen, Kristina, et al.
(författare)
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Laser capture microdissection (LCM) and whole genome amplification (WGA) of DNA from normal breast tissue - optimization for genome wide array analyses.
- 2011
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4, s. 69-69
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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)
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A ranking index for quality assessment of forensic DNA profiles
- 2010
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Ingår i: BMC Research Notes. - : BioMed Central Ltd. - 1756-0500. ; 3:290
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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)
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Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update
- 2008
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 1:49, s. 1-8
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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)
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Computational toxicology using the OpenTox application programming interface and Bioclipse
- 2011
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4:1, s. 487-
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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)
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Reliability and validity of motion analysis in children treated for congenital clubfoot according to the Clubfoot Assessment Protocol (CAP) using inexperienced assessors
- 2009
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 2
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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)
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Validation in Swedish of sydney swallow questionnaire.
- 2014
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 7:1
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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)
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The Libyan doctors' brain drain: an exploratory study.
- 2009
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 2:Dec 8
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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)
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Prophylactic treatment uptake and compliance with recommended follow up among HIV exposed infants : a retrospective study in Addis Ababa, Ethiopia
- 2011
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4, s. 563-563
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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)
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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
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 5
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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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11. |
- Butt, Salma, et al.
(författare)
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Breastfeeding in relation to risk of different breast cancer characteristics.
- 2014
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this present study was to examine duration of breastfeeding in relation to the risk of different subgroups of breast cancer. A prospective cohort, The Malmö Diet and Cancer study, including 14092 parous women, were followed during a mean of 10.2 years and a total of 424 incident breast cancers were diagnosed.
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12. |
- Butt, Salma, et al.
(författare)
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Genetic predisposition, parity, age at first childbirth and risk for breast cancer.
- 2012
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Recent studies have identified several single-nucleotide polymorphisms (SNPs) associated with the risk of breast cancer and parity and age at first childbirth are well established and important risk factors for breast cancer. The aim of the present study was to examine the interaction between these environmental factors and genetic variants on breast cancer risk.METHODS: The Malmö Diet and Cancer Study (MDCS) included 17 035 female participants, from which 728 incident breast cancer cases were matched to 1448 controls. The associations between 14 SNPs and breast cancer risk were investigated in different strata of parity and age at first childbirth. A logistic regression analysis for the per allele risk, adjusted for potential confounders yielded odds ratios (OR) with 95% confidence intervals (CI).RESULTS: Six of the previously identified SNPs showed a statistically significant association with breast cancer risk: rs2981582 (FGFR2), rs3803662 (TNRC9), rs12443621 (TNRC9), rs889312 (MAP3K1), rs3817198 (LSP1) and rs2107425 (H19). We could not find any statistically significant interaction between the effects of tested SNPs and parity/age at first childbirth on breast cancer risk after adjusting for multiple comparisons.CONCLUSIONS: The results of this study are in agreement with previous studies of null interactions between tested SNPs and parity/age at first childbirth with regard to breast cancer risk.
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13. |
- Ekelund, Ulf, et al.
(författare)
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Likelihood of acute coronary syndrome in emergency department chest pain patients varies with time of presentation
- 2012
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 5:420
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is a circadian and circaseptal (weekly) variation in the onset of acute coronary syndrome (ACS). The aim of this study was to elucidate whether the likelihood of ACS among emergency department (ED) chest pain patients varies with the time of presentation. Methods: All patients presenting to the Lund ED at Skåne University Hospital with chest pain or discomfort during 2006 and 2007 were retrospectively included. Age, sex, arrival time at the ED and discharge diagnose (ACS or not) were obtained from the electronic medical records. Results: There was a clear but moderate circadian variation in the likelihood of ACS among presenting chest pain patients, the likelihood between 8 and 10 am being almost twice as high as between 6 and 8 pm. This was mainly explained by a variation in the ACS likelihood in females and patients under 65 years, with no significant variation in males and patients over 65 years. There was no significant circaseptal variation in the ACS likelihood. Conclusions: Our results indicate that there is a circadian variation in the likelihood of ACS among ED chest pain patients, and suggest that physicians should consider the time of presentation to the ED when determining the likelihood of ACS.
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14. |
- Kaszuba, Elzbieta, et al.
(författare)
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Comparing impedance cardiography and echocardiography in the assessment of reduced left ventricular systolic function
- 2013
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 6:114, s. 1-5
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Tidskriftsartikel (refereegranskat)abstract
- Background An early and accurate diagnosis of chronic heart failure is a big challenge for a general practitioner. Assessment of left ventricular function is essential for the diagnosis of heart failure and the prognosis. A gold standard for identifying left ventricular function is echocardiography. Echocardiography requires input from specialized care and has a limited access in Swedish primary health care. Impedance cardiography (ICG) is a noninvasive and low-cost method of examination. The survey technique is simple and ICG measurement can be performed by a general practitioner. ICG has been suggested for assessment of left ventricular function in patients with heart failure. We aimed to study the association between hemodynamic parameters measured by ICG and the value of ejection fraction as a determinant of reduced left ventricular systolic function in echocardiography. Methods A non-interventional, observational study conducted in the outpatients heart failure unit. Thirty-six patients with the diagnosis of chronic heart failure were simultaneously examined by echocardiography and ICG. Distribution of categorical variables was presented as numbers. Distribution of continuous variables was presented as a mean and 95% Confidence Interval. Kruskal-Wallis test was used to compare variables and show differences between the groups. A p-value of <0.05 was considered significant. Results We found that three ICG parameters: pre-ejection fraction, left ventricular ejection time and systolic time ratio were significantly associated with ejection fraction measured by echocardiography. Conclusions The association which we found between EF and ICG parameters was not reported in previous studies. We found no association between EF and ICG parameters which were suggested previously as the determinants of reduced left ventricular systolic function. The knowledge concerning explanation of hemodynamic parameters measured by ICG that is available nowadays is not sufficient to adopt the method in practice and use it to describe left ventricular systolic dysfunction.
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15. |
- Larsson, Johanna, et al.
(författare)
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Chronic non-bloody diarrhoea: a prospective study in Malmö, Sweden, with focus on microscopic colitis.
- 2014
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Chronic non-bloody diarrhoea affects up to 5% of the population. Microscopic colitis is one of the most common causes, encompassing the subtypes collagenous colitis and lymphocytic colitis. The diagnosis of microscopic colitis is made by histological examination of colonic mucosal biopsy specimens. The aim of this investigation was to determine whether laboratory parameters or questions about disease history or concomitant disease could be helpful in discriminating patients with MC from those with a histologically normal colonic mucosa.
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16. |
- Lepsenyi, Mattias, et al.
(författare)
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Self-expanding metal stents in malignant colonic obstruction: experiences from Sweden.
- 2011
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Acute surgery in the management of malignant colonic obstruction is associated with high morbidity and mortality. The use of self-expanding metal stents (SEMS) is an alternative method of decompressing colonic obstruction. SEMS may allow time to optimize the patient and to perform preoperative staging, converting acute surgery into elective. SEMS is also proposed as palliative treatment in patients with contraindications to open surgery. Aim: To review our experience of SEMS focusing on clinical outcome and complications. The method used was a review of 75 consecutive trials at SEMS on 71 patients based on stent-protocols and patient charts. FINDINGS: SEMS was used for palliation in 64 (85%) cases and as a bridge to surgery in 11 (15%) cases. The majority of obstructions, 53 (71%) cases, were located in the recto-sigmoid. Technical success was achieved in 65 (87%) cases and clinical decompression was achieved in 60 (80%) cases. Reasons for technical failure were inability to cannulate the stricture in 5 (7%) cases and suboptimal SEMS placement in 3 (4%) cases. Complications included 4 (5%) procedure-related bowel perforations of which 2 (3%) patients died in junction to post operative complications. Three cases of bleeding after SEMS occurred, none of which needed invasive treatment. Five of the SEMS occluded. Two cases of stent erosion were diagnosed at the time of surgery. Average survival after palliative SEMS treatment was 6 months. CONCLUSION: Our results correspond well to previously published data and we conclude that SEMS is a relatively safe and effective method of treating malignant colonic obstruction although the risk of SEMS-related perforations has to be taken into account.
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17. |
- Pasupuleti, Mukesh, et al.
(författare)
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Antimicrobial activity of a C-terminal peptide from human extracellular superoxide dismutase
- 2009
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Ingår i: BMC research notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 2, s. 136-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Antimicrobial peptides (AMP) are important effectors of the innate immune system. Although there is increasing evidence that AMPs influence bacteria in a multitude of ways, bacterial wall rupture plays the pivotal role in the bactericidal action of AMPs. Structurally, AMPs share many similarities with endogenous heparin-binding peptides with respect to secondary structure, cationicity, and amphipathicity. FINDINGS: In this study, we show that RQA21 (RQAREHSERKKRRRESECKAA), a cationic and hydrophilic heparin-binding peptide corresponding to the C-terminal region of extracellular superoxide dismutase (SOD), exerts antimicrobial activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus subtilis and Candida albicans. The peptide was also found to induce membrane leakage of negatively charged liposomes. However, its antibacterial effects were abrogated in physiological salt conditions as well as in plasma. CONCLUSION: The results provide further evidence that heparin-binding peptide regions are multifunctional, but also illustrate that cationicity alone is not sufficient for AMP function at physiological conditions. However, our observation, apart from providing a link between heparin-binding peptides and AMPs, raises the hypothesis that proteolytically generated C-terminal SOD-derived peptides could interact with, and possibly counteract bacteria. Further studies are therefore merited to study a possible role of SOD in host defence.
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18. |
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19. |
- Thorlacius, Henrik, et al.
(författare)
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Cystic neuroendocrine tumor in the pancreas detected by endoscopic ultrasound and fine-needle aspiration: a case report.
- 2014
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 7:Aug 9
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Tidskriftsartikel (refereegranskat)abstract
- Pancreatic neuroendocrine tumors are typically solid neoplasms but in very rare cases present as cystic lesions. The diagnosis of cystic tumors in the pancreas is extremely difficult and the use of endoscopic ultrasound and fine-needle aspiration might be helpful in the work-up of patients with cystic neuroendocrine tumors in the pancreas.
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20. |
- Hedlund, Joel, et al.
(författare)
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BRICHOS - a superfamily of multidomain proteins with diverse functions.
- 2009
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Ingår i: BMC research notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 2, s. 180-
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Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT: BACKGROUND: The BRICHOS domain has been found in 8 protein families with a wide range of functions and a variety of disease associations, such as respiratory distress syndrome, dementia and cancer. The domain itself is thought to have a chaperone function, and indeed three of the families are associated with amyloid formation, but its structure and many of its functional properties are still unknown. FINDINGS: The proteins in the BRICHOS superfamily have four regions with distinct properties. We have analysed the BRICHOS proteins focusing on sequence conservation, amino acid residue properties, native disorder and secondary structure predictions. Residue conservation shows large variations between the regions, and the spread of residue conservation between different families can vary greatly within the regions. The secondary structure predictions for the BRICHOS proteins show remarkable coherence even where sequence conservation is low, and there seems to be little native disorder. CONCLUSIONS: The greatly variant rates of conservation indicates different functional constraints among the regions and among the families. We present three previously unknown BRICHOS families; group A, which may be ancestral to the ITM2 families; group B, which is a close relative to the gastrokine families, and group C, which appears to be a truly novel, disjoint BRICHOS family. The C-terminal region of group C has nearly identical sequences in all species ranging from fish to man and is seemingly unique to this family, indicating critical functional or structural properties.
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21. |
- Lövborg, Henrik, et al.
(författare)
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Structure-activity relationship analysis of cytotoxic cyanoguanidines : selection of CHS 828 as candidate drug.
- 2009
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Ingår i: BMC research notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 2, s. 114-
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Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT: BACKGROUND: N-(6-(4-chlorophenoxy)hexyl)-N'-cyano-N''-4-pyridyl guanidine) (CHS 828) is the first candidate drug from a novel group of anti-tumour agents - the pyridyl cyanoguanidines, shown to be potent compounds interfering with cellular metabolism (inhibition of nicotinamide phosphoribosyl transferase) and NF-kappaB signalling. Substituted cyanoguanidines are also found in anti-hypertensive agents such as the potassium channel opener pinacidil (N-cyano-N'-(4-pyridyl)-N''-(1,2,2-trimethylpropyl)guanidine) and histamine-II receptor antagonists (e.g. cimetidine, N-cyano-N'-methyl-N''-[2-[[(5-methylimidazol-4-yl]methyl]thio]ethyl)guanidine). In animal studies, CHS 828 has shown very promising activity, and phase I and II studies resulted in further development of a with a water soluble prodrug. FINDINGS: To study the structural requirements for cyanoguanidine cytotoxicity a set of 19 analogues were synthesized. The cytotoxic effects were then studied in ten cell lines selected for different origins and mechanisms of resistance, using the fluorometric microculture cytotoxicity assay (FMCA). The compounds showed varying cytotoxic activity even though the dose-response curves for some analogues were very shallow. Pinacidil and cimetidine were found to be non-toxic in all ten cell lines. Starting with cyanoguanidine as the crucial core it was shown that 4-pyridyl substitution was more efficient than was 3-pyridyl substitution. The 4-pyridyl cyanoguanidine moiety should be linked by an alkyl chain, optimally a hexyl, heptyl or octyl chain, to a bulky end group. The exact composition of this end group did not seem to be of crucial importance; when the end group was a mono-substituted phenyl ring it was shown that the preferred position was 4-substitution, followed by 3- and, finally, 2-substitution as the least active. Whether the substituent was a chloro, nitro or methoxy substituent seemed to be of minor importance. Finally, the activity patterns in the ten cell lines were compared. Substances with similar structures correlated well, whilst substances with large differences in molecular structure demonstrated lower correlation coefficients. CONCLUSION: According to this structure-activity relationship (SAR) study, CHS 828 meets the requirements for optimal cytotoxic activity for this class of compounds.
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22. |
- Monstein, Hans-Jurg, et al.
(författare)
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Application of PCR amplicon sequencing using a single primer pair in PCR amplification to assess variations in Helicobacter pylori CagA EPIYA tyrosine phosphorylation motifs
- 2010
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Ingår i: BMC Research Notes. - : BioMed Central. - 1756-0500. ; 3:35
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe presence of various EPIYA tyrosine phosphorylation motifs in the CagA protein of Helicobacter pylori has been suggested to contribute to pathogenesis in adults. In this study, a unique PCR assay and sequencing strategy was developed to establish the number and variation of cagA EPIYA motifs.FindingsMDA-DNA derived from gastric biopsy specimens from eleven subjects with gastritis was used with M13- and T7- sequence-tagged primers for amplification of the cagA EPIYA motif region. Automated capillary electrophoresis using a high resolution kit and amplicon sequencing confirmed variations in the cagA EPIYA motif region. In nine cases, sequencing revealed the presence of AB, ABC, or ABCC (Western type) cagA EPIYA motif, respectively. In two cases, double cagA EPIYA motifs were detected (ABC/ABCC or ABC/AB), indicating the presence of two H. pylori strains in the same biopsy.ConclusionAutomated capillary electrophoresis and amplicon sequencing using a single, M13- and T7-sequence-tagged primer pair in PCR amplification enabled a rapid molecular typing of cagA EPIYA motifs. Moreover, the techniques described allowed for a rapid detection of mixed H. pylori strains present in the same biopsy specimen.
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23. |
- Rundgren, Malin, et al.
(författare)
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Serum neuron specific enolase - impact of storage and measuring method.
- 2014
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Neuron specific enolase (NSE) is a recognized biomarker for assessment of neurological outcome after cardiac arrest, but its reliability has been questioned. Our aim was to investigate what influence storage of samples and choice of measuring methods may have on levels of NSE in peripheral blood.
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24. |
- Abraham-Nordling, Mirna, et al.
(författare)
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Model of the complex of Parathyroid hormone-2receptor and Tuberoinfundibular peptide of39 residues
- 2010
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Ingår i: BMC Reseach Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 3:270
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundWe aim to propose interactions between the parathyroid hormone-2 receptor (PTH2R) and its ligand the tuberoinfundibular peptide of 39 residues (TIP39) by constructing a homology model of their complex. The two related peptides parathyroid hormone (PTH) and parathyroid hormone related protein (PTHrP) are compared with the complex to examine their interactions.FindingsIn the model, the hydrophobic N-terminus of TIP39 is buried in a hydrophobic part of the central cavity between helices 3 and 7. Comparison of the peptide sequences indicates that the main discriminator between the agonistic peptides TIP39 and PTH and the inactive PTHrP is a tryptophan-phenylalanine replacement. The model indicates that the smaller phenylalanine in PTHrP does not completely occupy the binding site of the larger tryptophan residue in the other peptides. As only TIP39 causes internalisation of the receptor and the primary difference being an aspartic acid in position 7 of TIP39 that interacts with histidine 396 in the receptor, versus isoleucine/histidine residues in the related hormones, this might be a trigger interaction for the events that cause internalisation.ConclusionsA model is constructed for the complex and a trigger interaction for full agonistic activation between aspartic acid 7 of TIP39 and histidine 396 in the receptor is proposed.
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25. |
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26. |
- Aryal, Umesh R., 1973, et al.
(författare)
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Establishing a health demographic surveillance site in Bhaktapur district, Nepal : initial experiences and findings
- 2012
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Ingår i: BMC Research Notes. - : BioMed Central. - 1756-0500. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: A health demographic surveillance system (HDSS) provides longitudinal data regarding health and demography in countries with coverage error and poor quality data on vital registration systems due to lack of public awareness, inadequate legal basis and limited use of data in health planning. The health system in Nepal, a low-income country, does not focus primarily on health registration, and does not conduct regular health data collection. This study aimed to initiate and establish the first HDSS in Nepal.RESULTS: We conducted a baseline survey in Jhaukhel and Duwakot, two villages in Bhaktapur district. The study surveyed 2,712 households comprising a total population of 13,669. The sex ratio in the study area was 101 males per 100 females and the average household size was 5. The crude birth and death rates were 9.7 and 3.9/1,000 population/year, respectively. About 11% of births occurred at home, and we found no mortality in infants and children less than 5 years of age. Various health problems were found commonly and some of them include respiratory problems (41.9%); headache, vertigo and dizziness (16.7%); bone and joint pain (14.4%); gastrointestinal problems (13.9%); heart disease, including hypertension (8.8%); accidents and injuries (2.9%); and diabetes mellitus (2.6%). The prevalence of non-communicable disease (NCD) was 4.3% (95% CI: 3.83; 4.86) among individuals older than 30 years. Age-adjusted odds ratios showed that risk factors, such as sex, ethnic group, occupation and education, associated with NCD.CONCLUSION: Our baseline survey demonstrated that it is possible to collect accurate and reliable data in a village setting in Nepal, and this study successfully established an HDSS site. We determined that both maternal and child health are better in the surveillance site compared to the entire country. Risk factors associated with NCDs dominated morbidity and mortality patterns.
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27. |
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28. |
- Bölenius, Karin, et al.
(författare)
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A content validated questionnaire for assessment of self reported venous blood sampling practices
- 2012
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 5, s. 39-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Venous blood sampling is a common procedure in health care. It is strictly regulated by national and international guidelines. Deviations from guidelines due to human mistakes can cause patient harm. Validated questionnaires for health care personnel can be used to assess preventable "near misses"--i.e. potential errors and nonconformities during venous blood sampling practices that could transform into adverse events. However, no validated questionnaire that assesses nonconformities in venous blood sampling has previously been presented. The aim was to test a recently developed questionnaire in self reported venous blood sampling practices for validity and reliability.FINDINGS: We developed a questionnaire to assess deviations from best practices during venous blood sampling. The questionnaire contained questions about patient identification, test request management, test tube labeling, test tube handling, information search procedures and frequencies of error reporting. For content validity, the questionnaire was confirmed by experts on questionnaires and venous blood sampling. For reliability, test-retest statistics were used on the questionnaire answered twice. The final venous blood sampling questionnaire included 19 questions out of which 9 had in total 34 underlying items. It was found to have content validity. The test-retest analysis demonstrated that the items were generally stable. In total, 82% of the items fulfilled the reliability acceptance criteria.CONCLUSIONS: The questionnaire could be used for assessment of "near miss" practices that could jeopardize patient safety and gives several benefits instead of assessing rare adverse events only. The higher frequencies of "near miss" practices allows for quantitative analysis of the effect of corrective interventions and to benchmark preanalytical quality not only at the laboratory/hospital level but also at the health care unit/hospital ward.
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29. |
- Chatterjee, Koushik, et al.
(författare)
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Fas and FasL gene polymorphisms are not associated with cervical cancer but differ among Black and Mixed-ancestry South Africans
- 2009
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Ingår i: BMC research notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 2, s. 238-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Cervical cancer is one of the most important cancers in African women. Polymorphisms in the Fas (FasR) and Fas ligand (FasL) genes have been reported to be associated with cervical cancer in certain populations. This study investigated whether these polymorphisms are associated with cervical cancer or human papillomavirus (HPV) infection in South African women. FINDINGS: Participants were 447 women with invasive cervical cancer (106 black African and 341 women of mixed-ancestry) and 424 healthy women controls, matched by age, (101 black African and 323 women of mixed-ancestry) and domicile (rural or urban). Two polymorphisms in Fas gene (FasR-1377G/A, FasR-670A/G) and one in FasL gene (FasL844T/C) were genotyped by TaqMan. None of the polymorphisms, or the Fas haplotypes, showed a significant association with cervical cancer. There was also no association with HPV infection in the control group. However, on analysis of the control group, highly significant allele, genotype and haplotype differences were found between the two ethnic groups. There were generally low frequencies of FasR-1377A alleles, FasR-670A alleles and FasL-844C alleles in black women compared to the women of mixed-ancestry. CONCLUSION: This is the first study on the role of Fas and FasL polymorphisms in cervical cancer in African populations. Our results suggest that these SNPs are not associated with cervical cancer in these populations. The allele frequencies of the three SNPs differed markedly between the indigenous African black and mixed-ancestry populations.
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30. |
- Cipriano, Mariateresa, et al.
(författare)
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The influence of monoacylglycerol lipase inhibition upon the expression of epidermal growth factor receptor in human PC-3 prostate cancer cells.
- 2014
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Ingår i: BMC Research Notes. - : BioMed Central. - 1756-0500. ; 7, s. 441-447
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Tidskriftsartikel (refereegranskat)abstract
- Background: It has been reported that direct activation of the cannabinoid CB1 receptor in epidermal growth factor (EGR)-stimulated PC-3 prostate cancer cells results in an anti-proliferative effect accompanied by a down-regulation of EGF receptors (EGFR). In the present study, we investigated whether similar effects are seen following inhibition of the endocannabinoid hydrolytic enzyme monoacylglycerol lipase (MGL).Results: CB1 receptor expression levels were found to differ greatly between two experimental series conducted using PC-3 cells. The monoacylglycerol lipase inhibitor JZL184 increased levels of 2-arachidonoylglycerol in the PC-3 cells without producing changes in the levels of anandamide and related N-acylethanolamines. In the first series of experiments, JZL184 produced a small mitogenic effect for cells that had not been treated with EGF, whereas an anti-proliferative effect was seen for EGF-treated cells. An anti-proliferative effect for the EGF-treated cells was also seen with the CB receptor agonist CP55,940. In the second batch of cells, there was an interaction between JZL184 and CB1 receptor expression densities in linear regression analyses with EGFR expression as the dependent variable.Conclusions: Inhibition of MGL by JZL184 can affect EGFR expression. However, the use in our hands of PC-3 cells as a model to investigate the therapeutic potential of MGL inhibitors and related compounds is compromised by their variability of CB1 receptor expression.
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31. |
- Clendenen, Tess V, et al.
(författare)
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Temporal reliability of cytokines and growth factors in EDTA plasma
- 2010
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Ingår i: BMC research notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 3:1, s. 302-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Cytokines are involved in the development of chronic diseases, including cancer. It is important to evaluate the temporal reproducibility of cytokines in plasma prior to conducting epidemiologic studies utilizing these markers. FINDINGS: We assessed the temporal reliability of CRP, 22 cytokines and their soluble receptors (IL-1alpha, IL-1beta, IL-1Ra, IL-2, sIL-2R, IL-4, IL-5, IL-6, sIL-6R, IL-7, IL-8, IL-10, IL-12p40, IL-12p70, IL-13, IL-15, IL-17, TNFalpha, sTNF-R1, sTNF-R2, IFNalpha, IFNgamma) and eight growth factors (GM-CSF, EGF, bFGF, G-CSF, HGF, VEGF, EGFR, ErbB2) in repeated EDTA plasma samples collected an average of two years apart from 18 healthy women (age range: 42-62) enrolled in a prospective cohort study. We also estimated the correlation between serum and plasma biomarker levels using 18 paired clinical samples from postmenopausal women (age range: 75-86). Twenty-six assays were able to detect their analytes in at least 70% of samples. Of those 26 assays, we observed moderate to high intra-class correlation coefficients (ICCs)(ranging from 0.53-0.89) for 22 assays, and low ICCs (0-0.47) for four assays. Serum and plasma levels were highly correlated (r > 0.6) for most markers, except for seven assays (r < 0.5). CONCLUSIONS: For 22 of the 31 biomarkers, a single plasma measurement is a reliable estimate of a woman's average level over a two-year period.
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32. |
- Dauvrin, M., et al.
(författare)
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Health care for irregular migrants : Pragmatism across Europe. A qualitative study
- 2012
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 5, s. Art. no. 99-
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Tidskriftsartikel (refereegranskat)abstract
- Abstract. Background: Health services in Europe face the challenge of delivering care to a heterogeneous group of irregular migrants (IM). There is little empirical evidence on how health professionals cope with this challenge. This study explores the experiences of health professionals providing care to IM in three types of health care service across 16 European countries. Results: Semi-structured interviews were conducted with health professionals in 144 primary care services, 48 mental health services, and 48 Accident & Emergency departments (total n = 240). Although legal health care entitlement for IM varies across countries, health professionals reported facing similar issues when caring for IM. These issues include access problems, limited communication, and associated legal complications. Differences in the experiences with IM across the three types of services were also explored. Respondents from Accident & Emergency departments reported less of a difference between the care for IM patients and patients in a regular situation than did respondents from primary care and mental health services. Primary care services and mental health services were more concerned with language barriers than Accident & Emergency departments. Notifying the authorities was an uncommon practice, even in countries where health professionals are required to do this. Conclusions: The needs of IM patients and the values of the staff appear to be as important as the national legal framework, with staff in different European countries adopting a similar pragmatic approach to delivering health care to IM. While legislation might help to improve health care for IM, more appropriate organisation and local flexibility are equally important, especially for improving access and care pathways. © 2012 Dauvrin et al; licensee BioMed Central Ltd.
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33. |
- Dubois, Louise, et al.
(författare)
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Evaluating real-time immunohistochemistry on multiple tissue samples, multiple targets and multiple antibody labeling methods
- 2013
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 6, s. 542-
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundImmunohistochemistry (IHC) is a well-established method for the analysis of protein expression in tissue specimens and constitutes one of the most common methods performed in pathology laboratories worldwide. However, IHC is a multi-layered method based on subjective estimations and differences in staining and interpretation has been observed between facilities, suggesting that the analysis of proteins on tissue would benefit from protocol optimization and standardization. Here we describe how the emerging and operator independent tool of real-time immunohistochemistry (RT-IHC) reveals a time resolved description of antibody interacting with target protein in formalin fixed paraffin embedded tissue. The aim was to understand the technical aspects of RT-IHC, regarding generalization of the concept and to what extent it can be considered a quantitative method.ResultsThree different antibodies labeled with fluorescent or radioactive labels were applied on nine different tissue samples from either human or mouse, and the results for all RT-IHC analyses distinctly show that the method is generally applicable. The collected binding curves showed that the majority of the antibody-antigen interactions did not reach equilibrium within 3 hours, suggesting that standardized protocols for immunohistochemistry are sometimes inadequately optimized. The impact of tissue size and thickness as well as the position of the section on the glass petri dish was assessed in order for practical details to be further elucidated for this emerging technique. Size and location was found to affect signal magnitude to a larger extent than thickness, but the signal from all measurements were still sufficient to trace the curvature. The curvature, representing the kinetics of the interaction, was independent of thickness, size and position and may be a promising parameter for the evaluation of e.g. biopsy sections of different sizes.ConclusionsIt was found that RT-IHC can be used for the evaluation of a number of different antibodies and tissue types, rendering it a general method. We believe that by following interactions over time during the development of conventional IHC assays, it becomes possible to better understand the different processes applied in conventional IHC, leading to optimized assay protocols with improved sensitivity.
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34. |
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35. |
- Flot, Jean-François, et al.
(författare)
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Lophelia pertusa corals from the Ionian and Barents seas share identical nuclear ITS2 and near-identical mitochondrial genome sequences.
- 2013
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Lophelia pertusa is a keystone cold-water coral species with a widespread distribution. Due to the lack of a mitochondrial marker variable enough for intraspecific analyses, the population structure of this species has only been studied using ITS and microsatellites so far. We therefore decided to sequence and compare complete mitochondrial genomes from two distant L. pertusa populations putatively isolated from each other (in the Barents Sea off Norway and in the Mediterranean Sea off Italy) in the hope of finding regions variable enough for population genetic and phylogeographic studies. RESULTS: The mitogenomes of two L. pertusa individuals collected in the Mediterranean and Barents seas differed at only one position, which was a non-synonymous substitution, but comparison with another recently published L. pertusa mitochondrial genome sequence from Norway revealed 18 nucleotide differences. These included two synonymous and nine non-synonymous substitutions in protein-coding genes (dN/dS > 1): hence, the mitogenome of L. pertusa may be experiencing positive selection. To test for the presence of cryptic species, the mitochondrial control region and the nuclear ITS2 were sequenced for five individuals from each site: Italian and Norwegian populations turned out to share haplotypes of both markers, indicating that they belonged to the same species. CONCLUSIONS: L. pertusa corals collected 7,500 km apart shared identical nuclear ITS2 and near-identical mitogenomes, supporting the hypothesis of a recent connection between Lophelia reefs in the Mediterranean and in the Northern Atlantic. Multi-locus or population genomic approaches will be required to shed further light on the genetic connectivity between L. pertusa reefs across Europe; nevertheless, ITS2 and the mitochondrial control region may be useful markers for investigating the phylogeography and species boundaries of the keystone genus Lophelia across its worldwide area of distribution.
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36. |
- Grimby-Ekman, Anna, 1967, et al.
(författare)
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Simple neck pain questions used in surveys, evaluated in relation to health outcomes: a cohort study.
- 2012
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Ingår i: BMC research notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT: BACKGROUND: The high prevalence of pain reported in many epidemiological studies, and the degree to which this prevalence reflects severe pain is under discussion in the literature. The aim of the present study was to evaluate use of the simple neck pain questions commonly included in large epidemiological survey studies with respect to aspects of health. We investigated if and how an increase in number of days with pain is associated with reduction in health outcomes. METHODS: A cohort of university students (baseline age 19-25 years) were recruited in 2002 and followed annually for 4 years. The baseline response rate was 69% which resulted in 1200 respondents (627 women, 573 men). Participants were asked about present and past pain and perceptions of their general health, sleep disturbance, stress and energy levels, and general performance. The data were analyzed using a mixed model for repeated measurements and a random intercept logistic model. RESULTS: When reporting present pain, participants also reported lower prevalence of very good health, higher stress and sleep disturbance scores and lower energy score. Among those with current neck pain, additional questions characterizing the pain such as duration (categorized), additional pain sites and decreased general performance were associated with lower probability of very good health and higher amounts of sleep disturbance. Knowing about the presence or not of pain explains more of the variation in health between individuals, than within individuals. CONCLUSION: This study of young university students has demonstrated that simple neck pain survey questions capture features of pain that affect aspects of health such as perceived general health, sleep disturbance, mood in terms of stress and energy. Simple pain questions are more useful for group descriptions than for describing or following pain in an individual.
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37. |
- Guldbrandsson, K., et al.
(författare)
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Identification of potential opinion leaders in child health promotion in Sweden using network analysis
- 2012
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 5, s. Art. no. 424-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Opinion leaders are often local individuals with high credibility who can influence other people. Robust effects using opinion leaders in diffusing innovations have been shown in several randomized controlled trials, for example regarding sexually transmitted infections (STI), human immunodeficiency virus (HIV) prevention, mammography rates and caesarean birth delivery rates. In a Cochrane review 2010 it was concluded that the use of opinion leaders can successfully promote evidence-based practice. Thus, using opinion leaders within the public health sector might be one means to speed up the dissemination of health promoting and disease preventing innovations. Social network analysis has been used to trace and map networks, with focus on relationships and positions, in widely spread arenas and topics. The purpose of this study was to use social network analysis in order to identify potential opinion leaders at the arena of child health promotion in Sweden. Results: By using snowball technique a short e-mail question was spread in up to five links, starting from seven initially invited persons. This inquiry resulted in a network consisting of 153 individuals. The most often mentioned actors were researchers, public health officials and paediatricians, or a combination of these professions. Four single individuals were mentioned by five to seven other persons in the network. These individuals obviously possess qualities that make other professionals within the public health sector listen to and trust them. Conclusions: Social network analysis seemed to be a useful method to identify influential persons with high credibility, i.e. potential opinion leaders, at the arena of child health promotion in Sweden. If genuine opinion leaders could be identified directed measures can be carried out in order to spread new and relevant knowledge. This may facilitate for public health actors at the local, regional and national level to more rapidly progress innovations into everyday practice. However, effectiveness studies of opinion leaders in the public health sector still have to be performed. © 2012 Guldbrandsson et al.
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38. |
- Günther, Torsten, et al.
(författare)
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Improved haplotype-based detection of ongoing selective sweeps towards an application in Arabidopsis thaliana.
- 2011
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Ingår i: BMC research notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4, s. 232-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The increasing amount of genome information allows us to address various questions regarding the molecular evolution and population genetics of different species. Such genome-wide data sets including thousands of individuals genotyped at hundreds of thousands of markers require time-efficient and powerful analysis methods. Demography and sampling introduce a bias into present population genetic tests of natural selection, which may confound results. Thus, a modification of test statistics is necessary to introduce time-efficient and unbiased analysis methods.RESULTS: We present an improved haplotype-based test of selective sweeps in samples of unequally related individuals. For this purpose, we modified existing tests by weighting the contribution of each individual based on its uniqueness in the entire sample. In contrast to previous tests, this modified test is feasible even for large genome-wide data sets of multiple individuals. We utilize coalescent simulations to estimate the sensitivity of such haplotype-based test statistics to complex demographic scenarios, such as population structure, population growth and bottlenecks. The analysis of empirical data from humans reveals different results compared to previous tests. Additionally, we show that our statistic is applicable to empirical data from Arabidopsis thaliana. Overall, the modified test leads to a slight but significant increase of power to detect selective sweeps among all demographic scenarios.CONCLUSIONS: The concept of this modification might be applied to other statistics in population genetics to reduce the intrinsic bias of demography and sampling. Additionally, the combination of different test statistics may further improve the performance of tests for natural selection.
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39. |
- Hadziabdic, Emina, et al.
(författare)
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Arabic-speaking migrants’ attitudes, opinions, preferences and past experiences concerning the use of interpreters in healthcare : a postal cross-sectional survey
- 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
- BackgroundGood communication is an important prerequisite for equal treatment in a healthcare encounter. One way to overcome language barriers when patients and healthcare staff do not share the same language is to use a professional interpreter. Few previous studies have been found investigating the use of interpreters, and just one previous study from the perspective of European migrants, which showed that they perceived interpreters as a communication aid and a guide in the healthcare system as regards information and practical matters. No previous study has gathered quantitative information to focus on non-European migrants’ attitudes to the use of interpreters in healthcare encounters. Thus, the aim of this study was to investigate Arabic-speaking individuals’ attitudes, opinions, preferences and past experiences concerning the use of interpreters in healthcare in order to: (i) understand how persons’ expectations and concerns regarding interpreters may vary, both within and across cultural/linguistic populations; (ii) understand the consequences of diverse opinions/expectations for planning responsive services; and (iii) confirm findings from previous qualitative studies.MethodA postal cross-sectional study using a structured self-administered 51-item questionnaire was used to describe and document aspects of Arabic-speaking individuals’ attitudes to the use of interpreters in healthcare. The sample of 53 Arabic-speaking migrants was recruited from three different places. Participants were mostly born in Iraq and had a high level of education and were almost equally divided between genders. Data were analysed with descriptive statistics.ResultsThe main findings were that most of the participants perceived the interpreter’s role as being a communication aid and a practical aid, interpreting literally and objectively. Trust in the professional interpreter was related to qualification as an interpreter and personal contact with face-to-face interaction. The qualities of the desired professional interpreter were: a good knowledge of languages and medical terminology, translation ability, and sharing the same origin, dialect and gender as the patient.ConclusionThis study confirmed previous qualitative findings from European migrant groups with a different cultural and linguistic background. The study supports the importance of planning a good interpretation situation in accordance with individuals’ desire, irrespective of the migrant’s linguistic and cultural background, and using interpreters who interpret literally and objectively, who are highly trained with language skills in medical terminology, and with a professional attitude to promote communication, thus increasing cost-effective, high-quality individualized healthcare.
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40. |
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41. |
- Holmqvist, Marie, et al.
(författare)
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Transcript analysis of the extended hyp-operons in the cyanobacteria Nostoc sp. strain PCC 7120 and Nostoc punctiforme ATCC 29133
- 2011
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Ingår i: BMC Research Notes. - London : BioMed Central. - 1756-0500. ; 4:186
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The ability of cyanobacteria to capture solar energy, via oxygenic photosynthesis, and convert that energy to molecular hydrogen (H2) has made them an interesting group of organisms with potential as future energy producers. There are three types of enzymes directly involved in the cyanobacterial hydrogen metabolism; nitrogenases that produce H2 as a by-product when fixating atmospheric nitrogen, uptake hydrogenases that catalyze the oxidation of H2,thereby preventing energy losses from the cells, and bidirectional hydrogenases that has the capacity to both oxidize and reduce H2. Hydrogenases are complex metalloenzymes, and the insertion of ligands and correct folding of the proteins require assistance of accessory proteins, the Hyp proteins. Cyanobacterial hydrogenases are NiFe-type hydrogenases and consist of a large and a small subunit. Today, the maturation process of the large subunit has been uncovered to a large extent in cyanobacteria, mostly by analogy assumptions from studies done in other bacteria such as Escherichia coli but also from mutational analyses in cyanobacteria, while the maturation process of the small subunit is still unknown. Recently a set of genes, putatively involved in the maturation process of the small subunit, was discovered in Nostoc sp. PCC 7120 and Nostoc punctiforme ATCC 29133. These five ORFs, encoding unknown proteins, are located in between the uptake hydrogenase structural genes and the hyp-genes were shown to be transcribed together with the hyp-genes in Nostoc PCC 7120. The ORFs upstream the hyp-genes can be found in the same genomic arrangement in other filamentous, nitrogen fixing cyanobacterial strains but are interestingly missing in strains incapable of nitrogen fixation. In this study we have further investigated the function of the ORFs upstream the hyp-genes by studying their transcription pattern after nitrogen depletion in the filamentous, nitrogen fixing strains Nostoc PCC 7120 and N. punctiforme. The transcription pattern were compared to the transcription pattern of hupS and hoxY, encoding the uptake and bidirectional hydrogenase small subunits, nifD, encoding a nitrogenase subunit and hypC and hypF, encoding the maturation process accessory proteins HypC and HypF. All the five ORFs upstream the hyp-genes, in both organisms, were upregulated after nitrogen step down in accordance with the transcription pattern for hupS, nifD, hypC and hypF which support the theory that these genes might be involved in the maturation of the small subunit.
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42. |
- Höglund, Odd, et al.
(författare)
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Ligation of the spermatic cord in dogs with a self-locking device of a resorbable polyglycolic based co-polymer : feasibility and long-term follow-up study
- 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: New surgical techniques are developed to enable a quicker, easier and safer surgery with reduced risk of complications and shortened time needed for recovery. A resorbable device, a self-locking loop, was designed for surgical ligation. The objective of this pilot study was to investigate the feasibility of ligating the spermatic cord with the device, its biocompatibility and long-term resorption in dogs. Results: The device was made of a block co-polymer (glycolide and trimethylene carbonate), manufactured by injection moulding and consisted of a flexible band running through a case with a locking mechanism. Ten devices were tested for ligation of the spermatic cords in five dogs admitted for routine neutering. The dogs were monitored by physical examination and ultrasonography of the site of ligation, area of spermatic cord and medial iliac lymph nodes regularly until no hyperechoic remnants of the device or acoustic shadowing or local tissue reactions were observed. Haemostasis of the spermatic cords was achieved with the devices. On ultrasonography the devices were seen as hyperechoic structures for 2 months after neutering causing acoustic shadowing for 1 month. The dogs were monitored for 3 - 5 months after surgery. Gradual decrease in echogenicity and final disappearance of the hyperechoic structures suggested resorption. Macroscopic and histological post mortem examinations were performed in one dog at 3 months after surgery. Post mortem examination showed a tissue reaction of a suture granuloma that was restricted in extent at site of the device. Conclusions: The results of this pilot study suggest biocompatibility and indicate that ligation of the spermatic cord is feasible with the device.
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43. |
- Jacobsen, Mette, et al.
(författare)
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Characterisation of five candidate genes within the ETEC F4ab/ac candidate region in pigs
- 2011
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundEnterotoxigenic Escherichia coli (ETEC) that express the F4ab and F4ac fimbriae is a major contributor to diarrhoea outbreaks in the pig breeding industry, infecting both newborn and weaned piglets. Some pigs are resistant to this infection, and susceptibility is inherited as a simple dominant Mendelian trait. Indentifying the genetics behind this trait will greatly benefit pig welfare as well as the pig breeding industry by providing an opportunity to select against genetically susceptible animals, thereby reducing the number of diarrhoea outbreaks. The trait has recently been mapped by haplotype sharing to a 2.5 Mb region on pig chromosome 13, a region containing 18 annotated genes.FindingsThe coding regions of five candidate genes for susceptibility to ETEC F4ab/ac infection (TFRC, ACK1, MUC20, MUC4 and KIAA0226), all located in the 2.5 Mb region, were investigated for the presence of possible causative mutations. A total of 34 polymorphisms were identified in either coding regions or their flanking introns. The genotyping data for two of those were found to perfectly match the genotypes at the ETEC F4ab/ac locus, a G to C polymorphism in intron 11 of TFRC and a C to T silent polymorphism in exon 22 of KIAA0226. Transcriptional profiles of the five genes were investigated in a porcine tissue panel including various intestinal tissues. All five genes were expressed in intestinal tissues at different levels but none of the genes were found differentially expressed between ETEC F4ab/ac resistant and ETEC F4ab/ac susceptible animals in any of the tested tissues.ConclusionsNone of the identified polymorphisms are obvious causative mutations for ETEC F4ab/ac susceptibility, as they have no impact on the level of the overall mRNA expression nor predicted to influence the composition of the amino acids composition. However, we cannot exclude that the five tested genes are bona fide candidate genes for susceptibility to ETEC F4ab/ac infection since the identified polymorphism might affect the translational apparatus, alternative splice forms may exist and post translational mechanisms might contribute to disease susceptibility.
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44. |
- Jansson, Stefan P. O., 1959-, et al.
(författare)
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Interventions for lifestyle changes to promote weight reduction, a randomized controlled trial in primary health care
- 2013
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Ingår i: BMC Research Notes. - UK : BioMed Central Ltd.. - 1756-0500. ; 16:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Overweight and obesity are growing public health problems in high income countries and is now growing at a dramatic pace in low and middle income countries, particularly in urban settings. The aim of this trial was to examine the effects of a weight reduction program in adults and to determine whether or not a more extensive intervention was superior to ordinary care.Methods: Patients seeking advice for overweight/obesity or illness related to overweight/obesity at eight primary health care centers in Sweden were randomized either to intervention or control care groups with both groups given dietary advice and individualized information on increased regular physical activity. In the intervention group advice was more extensive and follow-up more frequent than in the control group during the study period of two years. Main outcome measure was reduction in body weight of five percent or more from study start.Results: From October 2004 to April 2006, 133 patients, 67 in the intervention group and 66 in the control group, were randomized over a period of 18 months. Target weight was achieved at 12 months by 26.7% of the patients in the intervention group compared with 18.4% in the control group (p = 0.335). There was an average absolute weight loss of 2.5 kg in the intervention group and 0.8 kg in the control group at 12 months as compared with the weight at study entry. There were no significant differences between the groups in quality of life, blood glucose and lipids. At 24 months target weight was achieved in 21.9% versus 15.6%, with an average weight reduction of 1.9 kg and 1.2 kg in the two groups, respectively.Conclusions: Promotion of a diet with limited energy intake, appropriate composition of food and increased physical activity had limited effects on body weight in a Swedish primary care setting. More extensive advice and more frequent visits made no significant difference to the outcome.
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45. |
- Kaplan-Sturk, Rebecka, et al.
(författare)
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Outcome of deliveries in healthy but obese women : obesity and delivery outcome
- 2013
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Ingår i: BMC Research Notes. - : BioMed Central. - 1756-0500. ; 6:50
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:Obesity among fertile women is a global problem. 25% of pregnant Swedish women are overweight at admission to the antenatal clinic and 12% of them are considered as obese. Previous studies have shown an increased risk of delivery complications with an elevated maternal BMI. The aim of this study was to evaluate delivery outcomes in relation to maternal BMI on admission to the antenatal clinic.A healthy group of 787 women with full-term pregnancies and spontaneous onset of labor were included in the study. Delivery outcome was assessed in relation to maternal BMI when attending the antenatal clinic.RESULTS:The results indicated that in deliveries where the maternal BMI was >30 a high frequency of abnormal CTG trace during the last 30 minutes of labor was shown. A blood sample for evaluation of risk of fetal hypoxia was performed in only eight percent of these deliveries. A spontaneous vaginal delivery without intervention was noted in 85.7%, and 12% of neonates were delivered with an adverse fetal outcome compared to 2.8% in the group with a maternal BMI<30 (p<0.001).CONCLUSION:These results indicate an increased risk at delivery for healthy, but obese women in labor. Furthermore, the delivery management may not always be optimal in these deliveries.
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46. |
- Kjellin, Lars, 1949-, et al.
(författare)
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Community treatment orders in a Swedish county : Applied as intended?
- 2014
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Ingår i: BMC Research Notes. - : BioMed Central. - 1756-0500. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Community treatment orders (CTOs) were legally implemented in psychiatry in Sweden in 2008, both in general psychiatry and in forensic psychiatric care. A main aim with the reform was to replace long leaves from compulsory psychiatric inpatient care with CTOs. The aims of the present study were to examine the use of compulsory psychiatric care before and after the reform and if this intention of the law reform was fulfilled.Methods: The study was based on register data from the computerized patient administrative system of Örebro County Council. Two periods of time, two years before (I) and two years after (II) the legal change, were compared. The Swedish civic registration number was used to connect unique individuals to continuous treatment episodes comprising different forms of legal status and to identify individuals treated during both time periods.Results: The number of involuntarily admitted patients was 524 in period I and 514 in period II. CTOs were in period II used on relatively more patients in forensic psychiatric care than in general psychiatry. In all, there was a 9% decrease from period I to period II in hospital days of compulsory psychiatric care, while days on leave decreased with 60%. The number of days on leave plus days under CTOs was 26% higher in period II than the number of days on leave in period I. Among patients treated in both periods, this increase was 43%. The total number of days under any form of compulsory care (in hospital, on leave, and under CTOs) increased with five percent. Patients with the longest leaves before the reform had more days on CTOs after the reform than other patients.Conclusions: The results indicate that the main intention of the legislator with introducing CTOs was fulfilled in the first two years after the reform in the studied county. At the same time the use of coercive psychiatric care outside hospital, and to some extent the total use of coercive in- and outpatient psychiatric care, increased. Adding an additional legal coercive instrument in psychiatry may increase the total use of coercion.
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47. |
- Kwamin, Francis, et al.
(författare)
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Interactions of extracts from selected chewing stick sources with Aggregatibacter actinomycetemcomitans
- 2012
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Ingår i: BMC Research Notes. - : BioMed Central. - 1756-0500. ; 5, s. 203-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Aggregatibacter actinomycetemcomitans produces a leukotoxin that activates a pro-inflammatory death of human monocytes/macrophages. A specific clone of this bacterium (JP2) has a 530-base pair deletion in the leukotoxin promoter gene that causes a significantly enhanced expression of leukotoxin. This specific clone of A. actinomycetemcomitans is common in some African populations and has a strong association with periodontal attachment loss in adolescents in these populations. Chewing sticks of plant origin are commonly used as oral hygiene tool in Africa, but their role as a therapeutic agent in periodontal disease is poorly investigated. RESULTS: Ethanol extracts were made from 7 common plants used as chewing sticks in West-Africa. None of the tested extracts inhibited growth of A. actinomycetemcomitans. However, extracts from Psidium guajava (Guava) completely neutralized the cell death and pro-inflammatory response of human leukocytes induced by the leukotoxin. None of the six other tested chewing stick extracts showed this effect. CONCLUSIONS: The discovery that extracts from Guava efficiently neutralizes A. actinomycetemcomitans leukotoxicity might lead to novel therapeutic agents and strategies for prevention and treatment of aggressive forms of periodontitis induced by infections with the highly leukotoxic JP2 clone of this bacterium.
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48. |
- Lysholm, Fredrik, et al.
(författare)
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An efficient simulator of 454 data using configurable statistical models
- 2011
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4:449
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundRoche 454 is one of the major 2nd generation sequencing platforms. The particular characteristics of 454 sequence data pose new challenges for bioinformatic analyses, e.g. assembly and alignment search algorithms. Simulation of these data is therefore useful, in order to further assess how bioinformatic applications and algorithms handle 454 data.FindingsWe developed a new application named 454sim for simulation of 454 data at high speed and accuracy. The program is multi-thread capable and is available as C++ source code or pre-compiled binaries. Sequence reads are simulated by 454sim using a set of statistical models for each chemistry. 454sim simulates recorded peak intensities, peak quality deterioration and it calculates quality values. All three generations of the Roche 454 chemistry ('GS20', 'GS FLX' and 'Titanium') are supported and defined in external text files for easy access and tweaking.ConclusionsWe present a new platform independent application named 454sim. 454sim is generally 200 times faster compared to previous programs and it allows for simple adjustments of the statistical models. These improvements make it possible to carry out more complex and rigorous algorithm evaluations in a reasonable time scale.
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49. |
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50. |
- Merrick, Daniel, et al.
(författare)
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Five years post whiplash injury : symptom and psychological factors in recovered versus non-recovered
- 2010
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Ingår i: BMC Research Notes. - : BioMed Central. - 1756-0500. ; 3, s. 190-
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Tidskriftsartikel (refereegranskat)abstract
- Background Few studies have focused on the differences between persons who are recovered after whiplash injury and those who suffer from persistent disability. The primary aim of this study was therefore to examine differences in symptoms, psychological factors and life satisfaction between subjects classified as recovered and those with persistent disability five years after whiplash injury based on the Neck Disability Index (NDI). Methods A set of questionnaires was answered by 158 persons (75 men, 83 women) to assess disability (NDI), pain intensity (VAS), whiplash-related symptoms (Rivermead Post-Concussion Symptoms Questionnaire, RPQ), post-traumatic stress (Impact of Event Scale, IES), depression (Beck's depression inventory, BDI) and life satisfaction (LiSat-11). The participants were divided into three groups based on the results of the NDI: recovered (34.8%), mild disability (37.3%) and moderate/severe disability (27.3%). Results The moderate/severe group reported significantly higher VAS, BDI and IES scores and lower level of physical health and psychological health compared to the mild and the recovered groups. Less significant differences were reported between the mild and the recovered groups. Conclusions The group with the highest disability score reported most health problems with pain, symptoms, depression, post-traumatic stress and decreased life satisfaction. These findings indicate that classifying these subjects into subgroups based on disability levels makes it possible to optimize the management and treatment after whiplash injury.
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