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Search Results: 1 - 10 of 4962 matches for " Andersson Bj?rn "
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FAAST: Flow-space Assisted Alignment Search Tool
Fredrik Lysholm, Bjrn Andersson, Bengt Persson
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-293
Abstract: We suggest a novel algorithm for calculating the optimal local alignment which utilises flowpeak information in order to improve alignment accuracy. Flowpeak information can be retained from a 454 sequencing run through interpretation of the binary SFF-file format. This novel algorithm has been implemented in a program named FAAST (Flow-space Assisted Alignment Search Tool).We present and discuss the results of simulations that show that FAAST, through the use of the novel algorithm, can gain several percentage points of accuracy compared to Smith-Waterman-Gotoh alignments, depending on the 454 data quality. Furthermore, through an efficient multi-thread aware implementation, FAAST is able to perform these high quality alignments at high speed.The tool is available at http://www.ifm.liu.se/bioinfo/ webciteThe nature of DNA sequencing has taken a dramatic turn in the last few years, most notably improved through the development and broad use of 2nd generation sequencing methods. The first 2nd generation sequencing method was 454 sequencing, introduced in 2005 with the GS20 sequencing machine which produced 20 million base-pairs (Mbp) per run [1]. 454 sequencing has since been improved steadily both regarding quality and throughput, and the GS FLX Titanium, introduced in 2008, produces 500 Mbp per run, as reads of approximately 350 bp [2]. Although, since 2005, other 2nd generation sequencing methods have emerged, 454 still produces the longest reads and is one of the most widely used platforms. The long reads produced by 454 sequencing makes the method especially attractive for metagenomic sequencing, where the sample is highly complex and overlapping reads are more rare. The enormous technology improvements represented by novel sequencing technologies do not only enable many new studies but also poses great challenges in terms of processing the sequence data. The major underlying technology for data processing is sequence alignment, which plays a key part in all ste
An efficient simulator of 454 data using configurable statistical models
Fredrik Lysholm, Bjrn Andersson, Bengt Persson
BMC Research Notes , 2011, DOI: 10.1186/1756-0500-4-449
Abstract: We 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.We 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.The introduction of 2nd generation sequencing techniques has resulted in a myriad of new large DNA sequencing projects, many of which have posed new challenges for bioinformatics. Roche 454 is one of the major 2nd generation sequencing platforms. The 454 instruments use a type of pyrosequencing chemistry, where the complementary strand is elongated through repeated cycles, each using one of the four nucleotides (flows). The complementary strand is elongated in the absence of a terminator, and homopolymer lengths are estimated by the light intensity recorded. As a consequence, homopolymer length uncertainties sometimes occur, especially at long homopolymer stretches [1]. This specific aspect of 454 data poses new challenges for downstream bioinformatic applications, such as assembly and alignment search algorithms [2-4]. Simulation of sequence data is an important and extensively used tool for assessing how bioinformatic applications and algorithms handle sequence data. The first software that was developed for simulation of 454 data was MetaSIM [5], which provided simulated data using the statistical distrib
Cloning of somatolactin alpha, beta forms and the somatolactin receptor in Atlantic salmon: Seasonal expression profile in pituitary and ovary of maturing female broodstock
Susana Benedet, Bjrn Bj?rnsson, Geir Taranger, Eva Andersson
Reproductive Biology and Endocrinology , 2008, DOI: 10.1186/1477-7827-6-42
Abstract: Atlantic salmon Sl alpha, Sl beta and slr cDNAs were cloned using a PCR approach. Gene expression of Sl alpha, SL beta and slr was studied using RTqPCR over a 17 month period encompassing pre-vitellogenesis, vitellogenesis, ovulation and post ovulation in salmon females. Histological examination of ovarian samples allowed for the classification according to the degree of follicle maturation into oil drop, primary, secondary or tertiary yolk stage.The mature peptide sequences of Sl alpha, Sl beta and slr are highly similar to previously cloned salmonid forms and contained the typical motifs. Phylogenetic analysis of Atlantic salmon Sl alpha and Sl beta shows that these peptides group into the two Sl clades present in some fish species. The Atlantic salmon slr grouped with salmonid slr amongst so-called type I ghr. An increase in pituitary Sl alpha and Sl beta transcripts before and during spawning, with a decrease post-ovulation, and a constant expression level of ovarian slr were observed. There was also a transient increase in Sl alpha and Sl beta in May prior to transfer from seawater to fresh water and ensuing fasting.The up-regulation of Sl alpha and Sl beta during vitellogenesis and spawning, with a subsequent decrease post-ovulation, supports a role for Sl during gonadal growth and spawning. Sl could also be involved in calcium/phosphate mobilization associated with vitellogenesis or have a role in energy homeostasis associated with lipolysis during fasting. The up-regulation of both Sl alpha and Sl beta prior to fasting and freshwater transfer, suggests a role for Sl linked to reproduction that may be independent of the maturation induced fasting.Somatolactin (Sl) is a peptide hormone exclusive to fish, and belongs to the class I helical cytokine family which includes growth hormone (Gh), prolactin (Prl) and leptin [1-3]. Two distinct forms coded by separate genes and produced in different cells in the pars intermedia of the pituitary have been isolated: Sl a
Computational Resources in Infectious Disease: Limitations and Challenges
Eva C. Berglund,Bjrn Nystedt,Siv G. E. Andersson
PLOS Computational Biology , 2009, DOI: 10.1371/journal.pcbi.1000481
Comparative evaluation of treatment with low-dose aspirin plus dipyridamole versus aspirin only in patients with acute ischaemic stroke
Arnarsdottir Lola,Hjalmarsson Clara,Bokemark Lena,Andersson Bjrn
BMC Neurology , 2012, DOI: 10.1186/1471-2377-12-67
Abstract: Background Previous studies have suggested that pre-stroke treatment with low-dose aspirin (A) could reduce the severity of acute ischaemic stroke, but less is known on the effect of pre-stroke treatment with a combination of aspirin and dipyridamole (A + D) and post-stroke effects of these drugs. The aim of the present study was to evaluate the effect of this drug combination on acute and long-term prognosis of ischaemic stroke. Methods Patients without atrial fibrillation admitted to the stroke unit with acute ischaemic stroke (n = 554) or TIA (n = 108) were studied during acute hospital care and up to 12 months after discharge from hospital. Results Prior to acute stroke 62 patients were treated with A + D while 247 patients were treated with A only. No beneficial effects of the combination A + D compared to A only were noted on stroke severity and/or acute in-hospital mortality. However, survival analysis by Cox-proportional hazard model demonstrated lower 12-months all-cause mortality in patients discharged with A + D (n = 275) compared with patients on A only (HR, 0.52; CI, 0.32-0.86; p = 0.011; n = 262) after adjusting for age, baseline NIHSS, previous stroke, previous myocardial infarction and type 2 diabetes. We also noted a tendency towards lower all-cause mortality at 3 months with use of A + D, but this was not statistically significant (p = 0.12). Conclusions Pre-stroke treatment with a combination of low-dose A + D does not reduce the severity of acute stroke, nor does it reduce the acute in-hospital mortality. However, treatment with A + D at discharge from hospital is seemingly associated with lower long-term mortality compared with A only, contrary to the results from previous randomised studies. However, our results must be interpreted with extreme caution considering the non-randomised study design.
The Role of Prestroke Glycemic Control on Severity and Outcome of Acute Ischemic Stroke
Clara Hjalmarsson,Karin Manhem,Lena Bokemark,Bjrn Andersson
Stroke Research and Treatment , 2014, DOI: 10.1155/2014/694569
Abstract: Background/Aim. Relatively few studies have investigated the association of prestroke glycemic control and clinical outcome in acute ischemic stroke (IS) patients, regardless of presence of diabetes mellitus (DM). The aim of this study was to investigate the importance of prestroke glycemic control on survival, stroke severity, and functional outcome of patients with acute IS. Methods. We performed a retrospective survival analysis of 501 patients with IS admitted to Sahlgrenska University Hospital from February 15, 2005, through May 31, 2009. The outcomes of interest were acute and long-term survival; the stroke severity (NIHSS) and the functional outcome, mRS, at 12 months. Results. HbA1c was a good predictor of acute (HR 1.45; CI, 1.09 to 1.93, ) and long-term mortality (HR 1.29; CI 1.03 to 1.62; ). Furthermore, HbA1c >6% was significantly correlated with acute stroke severity (OR 1.29; CI 1.01 to 1.67; ) and predicted worse functional outcome at 12 months (OR 2.68; CI 1.14 to 6.03; ). Conclusions. Our study suggests that poor glycemic control (baseline HbA1c) prior to IS is an independent risk factor for poor survival and a marker for increased stroke severity and unfavorable long-term functional outcome. 1. Introduction Hyperglycemia (HG) in relation to acute IS is common both in patients with and in patients without a diagnosis of DM, and it has been suggested to worsen survival. However, recent results from several clinical studies indicate that particularly patients with stroke and stress HG, but not diabetes, have increased mortality [1–3]. On the contrary, older data by Woo et al. [4] found that patients with acute IS and similar glucose concentrations had similar outcome regardless of whether they had diabetes or not. According to a review published by Capes et al. [5], acute HG predicted increased risk of in-hospital mortality after ischemic stroke (IS) in nondiabetic patients and increased risk of poor functional recovery in nondiabetic stroke survivors. The recent results of Nardi et al. [2] are also in line with this conclusion. In a study published in 2012, Hu et al. [1] evaluated the effects of HG and prestroke glycemic control, as measured by HbA1c, on all-cause and cardiovascular mortality among 1277 IS patients and found a significant association between initial glucose level and mortality in nondiabetic patients. Surprisingly, they also found that DM patients with HbA1c <7.0% had a higher incidence rate of all-cause and cardiovascular death than those with HbA1c ≥7%. Contradictory data have been published by Kamouchi et al. in 2011,
Cost-effectiveness of internet-based cognitive behavior therapy for irritable bowel syndrome: results from a randomized controlled trial
Erik Andersson, Brjánn Ljótsson, Filip Smit, Bjrn Paxling, Erik Hedman, Nils Lindefors, Gerhard Andersson, Christian Rück
BMC Public Health , 2011, DOI: 10.1186/1471-2458-11-215
Abstract: Participants (N = 85) with IBS were recruited through self-referral and were assessed via a telephone interview and self-report measures on the internet. Participants were randomized to internet-delivered CBT or to a discussion forum. Economic data was assessed at pre-, post- and at 3-month and 1 year follow-up.Significant cost reductions were found for the treatment group at $16,806 per successfully treated case. The cost reductions were mainly driven by reduced work loss in the treatment group. Results were sustained at 3-month and 1 year follow-up.Internet-delivered CBT appears to generate health gains in IBS treatment and is associated with cost-savings from a societal perspective.Irritable bowel syndrome (IBS) is a highly prevalent gastrointestinal disorder [1] that is associated with production losses [2,3] and increased levels of health service utilization [3,4]. The high prevalence rate combined with the costs associated for each afflicted individual makes IBS a considerable economic burden for society. Research indicates that psychological interventions - such as cognitive behavior therapy (CBT), hypnotherapy and psychodynamic therapy - can be effective in reducing IBS symptoms [5]. In addition, there is some evidence indicating that psychological treatments are cost-effective. In a study by Creed et al. [6], 171 patients with IBS were randomized to receive either 8 sessions of individual psychodynamic therapy, paroxetine, or care as usual. At one-year follow-up, the psychotherapy condition was associated with significant reductions in health care consumption when compared to care as usual, whereas the paroxetine group did not show a similar reduction. In a study by McCrone et al. [7], CBT was found to have a reasonable short-term cost-effectiveness but not beyond 3-month follow-up. In summary, although psychological treatments are effective in reducing IBS symptoms there is insufficient evidence of their cost-effectiveness.Our research group has recently c
Internet-based cognitive behavior therapy for obsessive compulsive disorder: A pilot study
Erik Andersson, Brjánn Ljótsson, Erik Hedman, Viktor Kaldo, Bjrn Paxling, Gerhard Andersson, Nils Lindefors, Christian Rück
BMC Psychiatry , 2011, DOI: 10.1186/1471-244x-11-125
Abstract: An open trial where patients (N = 23) received a 15-week ICBT program with therapist support consisting of psychoeducation, cognitive restructuring and exposure with response prevention. The primary outcome was the Yale-Brown Obsessive Compulsive Scale (Y-BOCS), which was assessed by a psychiatrist before and immediately after treatment. Secondary outcomes were self-rated measures of OCD symptoms, depressive symptoms, general functioning, anxiety and quality of life. All assessments were made at baseline and post-treatment.All participants completed the primary outcome measure at all assessment points. There were reductions in OCD symptoms with a large within-group effect size (Cohen's d = 1.56). At post-treatment, 61% of participants had a clinically significant improvement and 43% no longer fulfilled the diagnostic criteria of OCD. The treatment also resulted in statistically significant improvements in self-rated OCD symptoms, general functioning and depression.ICBT with therapist support reduces OCD symptoms, depressive symptoms and improves general functioning. Randomized trials are needed to confirm the effectiveness of this new treatment format.ClinicalTrials.gov: NCT01348529Obsessive compulsive disorder (OCD) is a chronic condition characterized by obsessions and/or compulsions (e.g. fear of dirt, need for symmetry, compulsory checking) [1]. OCD is associated with lowered quality of life, social isolation [1] and a large economic burden on society [2]. The lifetime prevalence is estimated to be 2-3% [3]. First line treatments are serotonin reuptake inhibitors and cognitive behavior therapy (CBT) [4]. Although there is substantial evidence for the effectiveness of CBT [5], there is generally limited access to CBT therapists [6,7]. Therefore, as evidence-based psychological treatment is scarce, it is essential to develop more time- and cost-efficient treatments for OCD patients who do not receive CBT. Self-help treatments have the potential to reduce therapist
The Dual Origin of the Yeast Mitochondrial Proteome
Olof Karlberg,Bj rn Canb ck,Charles G. Kurland,Siv G. E. Andersson
Comparative and Functional Genomics , 2000, DOI: 10.1002/1097-0061(20000930)17:3<170::aid-yea25>3.0.co;2-v
Abstract: We propose a scheme for the origin of mitochondria based on phylogenetic reconstructions with more than 400 yeast nuclear genes that encode mitochondrial proteins. Half of the yeast mitochondrial proteins have no discernable bacterial homologues, while one-tenth are unequivocally of α-proteobacterial origin. These data suggest that the majority of genes encoding yeast mitochondrial proteins are descendants of two different genomic lineages that have evolved in different modes. First, the ancestral free-living α-proteobacterium evolved into an endosymbiont of an anaerobic host. Most of the ancestral bacterial genes were lost, but a small fraction of genes supporting bioenergetic and translational processes were retained and eventually transferred to what became the host nuclear genome. In a second, parallel mode, a larger number of novel mitochondrial genes were recruited from the nuclear genome to complement the remaining genes from the bacterial ancestor. These eukaryotic genes, which are primarily involved in transport and regulatory functions, transformed the endosymbiont into an ATP-exporting organelle.
Analyses of an Expressed Sequence Tag Library from Taenia solium, Cysticerca
Jonas Lundstr?m,Fernando Salazar-Anton,Ellen Sherwood,Bjrn Andersson,Johan Lindh
PLOS Neglected Tropical Diseases , 2010, DOI: 10.1371/journal.pntd.0000919
Abstract: Background Neurocysticercosis is a disease caused by the oral ingestion of eggs from the human parasitic worm Taenia solium. Although drugs are available they are controversial because of the side effects and poor efficiency. An expressed sequence tag (EST) library is a method used to describe the gene expression profile and sequence of mRNA from a specific organism and stage. Such information can be used in order to find new targets for the development of drugs and to get a better understanding of the parasite biology. Methods and Findings Here an EST library consisting of 5760 sequences from the pig cysticerca stage has been constructed. In the library 1650 unique sequences were found and of these, 845 sequences (52%) were novel to T. solium and not identified within other EST libraries. Furthermore, 918 sequences (55%) were of unknown function. Amongst the 25 most frequently expressed sequences 6 had no relevant similarity to other sequences found in the Genbank NR DNA database. A prediction of putative signal peptides was also performed and 4 among the 25 were found to be predicted with a signal peptide. Proposed vaccine and diagnostic targets T24, Tsol18/HP6 and Tso31d could also be identified among the 25 most frequently expressed. Conclusions An EST library has been produced from pig cysticerca and analyzed. More than half of the different ESTs sequenced contained a sequence with no suggested function and 845 novel EST sequences have been identified. The library increases the knowledge about what genes are expressed and to what level. It can also be used to study different areas of research such as drug and diagnostic development together with parasite fitness via e.g. immune modulation.
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