Articles from BioMed Central


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  • Kagambèga, Assèta; Lienemann, Taru; Frye, Jonathan G; Barro, Nicolas; Haukka, Kaisa (BioMed Central, 2018)
    Abstract Background Multidrug-resistant Salmonella is an important cause of morbidity and mortality in developing countries. The aim of this study was to characterize and compare multidrug-resistant Salmonella enterica serovar Typhimurium isolates from patients and poultry feces. Methods Salmonella strains were isolated from poultry and patients using standard bacteriological methods described in previous studies. The strains were serotype according to Kaufmann-White scheme and tested for antibiotic susceptibility to 12 different antimicrobial agents using the disk diffusion method. The whole genome of the S. Typhimurium isolates was analyzed using Illumina technology and compared with 20 isolates of S. Typhimurium for which the ST has been deposited in a global MLST database.The ResFinder Web server was used to find the antibiotic resistance genes from whole genome sequencing (WGS) data. For comparative genomics, publicly available complete and draft genomes of different S. Typhimurium laboratory-adapted strains were downloaded from GenBank. Results All the tested Salmonella serotype Typhimurium were multiresistant to five commonly used antibiotics (ampicillin, chloramphenicol, streptomycin, sulfonamide, and trimethoprim). The multilocus sequence type ST313 was detected from all the strains. Our sequences were very similar to S. Typhimurium ST313 strain D23580 isolated from a patient with invasive non-typhoid Salmonella (NTS) infection in Malawi, also located in sub-Saharan Africa. The use of ResFinder web server on the whole genome of the strains showed a resistance to aminoglycoside associated with carriage of the following resistances genes: strA, strB, and aadA1; resistance to β-lactams associated with carriage of a bla TEM-1B genes; resistance to phenicol associated with carriage of catA1 gene; resistance to sulfonamide associated with carriage of sul1 and sul2 genes; resistance to tetracycline associated with carriage of tet B gene; and resistance to trimethoprim associated to dfrA1 gene for all the isolates. Conclusion The poultry and human isolates were genetically similar showing a potential food safety risk for consumers. Our finding of multidrug-resistant S. Typhimurium ST313 in poultry feces calls for further studies to clarify the potential reservoirs of this emerging pathogen.
  • Niimura del Barrio, Maria C; David, Florent; Hughes, J. M L; Clifford, David; Wilderjans, Hans; Bennett, Rachel (BioMed Central, 2018)
    Abstract Background The mortality rate of horses undergoing general anaesthesia is high when compared to humans or small animal patients. One of the most critical periods during equine anaesthesia is recovery, as the horse attempts to regain a standing position. This study was performed in a private equine practice in Belgium that uses a purpose-designed one-man (head and tail) rope recovery system to assist the horse during the standing process. The main purpose of the retrospective study was to report and analyse complications and the mortality rate in horses during recovery from anaesthesia using the described recovery system. Information retrieved from the medical records included patient signalment, anaesthetic protocol, duration of anaesthesia, ASA grade, type of surgery, recovery time and complications during recovery. Sedation was administered to all horses prior to recovery with the rope system. Complications were divided into major complications in which the horse was euthanized and minor complications where the horse survived. Major complications were further subdivided into those where the rope system did not contribute to the recovery complication (Group 1) and those where it was not possible to determine if the rope system was of any benefit (Group 2). Results Five thousand eight hundred fifty two horses recovered from general anaesthesia with rope assistance. Complications were identified in 30 (0.51%). Major complications occurred in 12 horses (0.20%) of which three (0.05%) were assigned to Group 1 and nine (0.15%) to Group 2. Three horses in Group 2 suffered musculoskeletal injuries (0.05%). Eighteen horses (0.31%) suffered minor complications, of which five (0.08%) were categorised as failures of the recovery system. Conclusions This study reports the major and minor complication and mortality rate during recovery from anaesthesia using a specific type of rope recovery system. Mortality associated with the rope recovery system was low. During recovery from anaesthesia this rope system may reduce the risk of lethal complications, particularly major orthopaedic injuries.
  • Taponen, Saara; Lehtimäki, Lauri; Karvala, Kirsi; Luukkonen, Ritva; Uitti, Jukka (BioMed Central, 2018)
    Abstract Background Asthmatics confront inconveniences in working life that make it more difficult to pursue a sustainable career, such as unemployment and work disability. Ways of dealing with these inconveniences may be career changes. More needs to be known about the backgrounds and consequences of career changes among asthmatics, especially their relation to asthma or a change in asthma symptoms. The aim of this study was to compare earlier career changes of adults with asthma who are working full time to those who have drifted away from active working life because of work disability, unemployment or early retirement. The frequency of having changed tasks, work place or occupation, whether the changes had been driven by asthma and furthermore, whether the changes had affected their asthma symptoms were investigated. Methods In this population-based survey study, all patients with reimbursement rights for asthma aged 20–65 years in the city of Tampere (total population 190,000), Finland (n = 2613) were recruited. The questionnaire was sent in October 2000 and the response rate was 79%. The questionnaire included questions e.g. on changing tasks, work place and occupation, whether these changes were driven by asthma or associated with change of asthma symptoms. The respondents were divided into four groups: working full-time, work disability, unemployed and retired due to age. We applied ANOVA with Dunnet’s post-test (variances were not equal between the groups) for a continued variable age and Chi-squared tests for categorical variables. Logistic regression models were built using unemployed vs. full-time work or work disability vs. full-time work as an outcome variable. A p-value of <.05 was considered statistically significant. Results Adults with asthma working full time had more often made changes in their career, but not as often driven by asthma as those with current work disability. The reason for changing work place compared to full-time workers (24.9%) was more often mainly or partly due to asthma among those with work disability (47.9%, p < 0.001) and the unemployed (43.3%, p = 0.006). Of those who made career changes because of asthma, a major proportion (over 67%) reported relief in asthma symptoms. Changing tasks (OR 5.8, 95% CI 1.9–18.0, for unemployment vs. full-time work), work place (OR 2.8, 95% CI 1.1–7.0, for work disability vs. full-time work and OR 2.6, 95% CI 1.3–5.4, for unemployment vs. full-time work) or occupation (OR 2.7, 95% CI 1.2–6.0, for unemployment vs. full-time work) mainly because of asthma was associated with an elevated risk for undesirable employment status even after adjusting for age, gender, smoking and professional status. Conclusions Career changes that were made mainly because of asthma were associated with undesirable employment status in this study. However, asthma symptoms were relieved after career changes especially among those who reported asthma to be the reason for the change. In addition to proper treatment and counselling of asthma patients towards applicable area of work or study, it may be beneficial to support early career changes in maintaining sustainable working careers among adults with asthma.
  • Järvinen, Tommi; Ilonen, Ilkka; Kauppi, Juha; Salo, Jarmo; Räsänen, Jari (BioMed Central, 2018)
    Abstract Background Nutritional deficits, cachexia, and sarcopenia are extremely common in esophageal cancer. The aim of this article was to assess the effect of loss of skeletal muscle mass during neoadjuvant treatment on the prognosis of esophageal cancer patients. Methods Esophageal cancer patients (N = 115) undergoing neoadjuvant therapy and surgery between 2010 and 2014 were identified from our surgery database and retrospectively analyzed. Computed tomography imaging of the total cross-sectional muscle tissue measured at the third lumbar level defined the skeletal muscle index, which defined sarcopenia (SMI < 52.4 cm2/m2 for men and < 38.5 cm2/m2 for women). Images were collected before and after neoadjuvant treatments. Results Sarcopenia in preoperative imaging was prevalent in 92 patients (80%). Median overall survival was 900 days (interquartile range 334–1447) with no difference between sarcopenic (median = 900) and non-sarcopenic (median = 914) groups (p = 0.872). Complication rates did not differ (26.1% vs 32.6%, p = 0.725). A 2.98% decrease in skeletal muscle index during neoadjuvant treatment correlated with poor 2-year survival (log-rank p = 0.04). Conclusion Loss of skeletal muscle tissue during neoadjuvant treatment correlates with worse overall survival.
  • Kjällquist, Una; Erlandsson, Rikard; Tobin, Nicholas P; Alkodsi, Amjad; Ullah, Ikram; Stålhammar, Gustav; Karlsson, Eva; Hatschek, Thomas; Hartman, Johan; Linnarsson, Sten; Bergh, Jonas (BioMed Central, 2018)
    Abstract Background Tumor heterogeneity in breast cancer tumors is today widely recognized. Most of the available knowledge in genetic variation however, relates to the primary tumor while metastatic lesions are much less studied. Many studies have revealed marked alterations of standard prognostic and predictive factors during tumor progression. Characterization of paired primary- and metastatic tissues should therefore be fundamental in order to understand mechanisms of tumor progression, clonal relationship to tumor evolution as well as the therapeutic aspects of systemic disease. Methods We performed full exome sequencing of primary breast cancers and their metastases in a cohort of ten patients and further confirmed our findings in an additional cohort of 20 patients with paired primary and metastatic tumors. Furthermore, we used gene expression from the metastatic lesions and a primary breast cancer data set to study the gene expression of the AKAP gene family. Results We report that somatic mutations in A-kinase anchoring proteins are enriched in metastatic lesions. The frequency of mutation in the AKAP gene family was 10% in the primary tumors and 40% in metastatic lesions. Several copy number variations, including deletions in regions containing AKAP genes were detected and showed consistent patterns in both investigated cohorts. In a second cohort containing 20 patients with paired primary and metastatic lesions, AKAP mutations showed an increasing variant allele frequency after multiple relapses. Furthermore, gene expression profiles from the metastatic lesions (n = 120) revealed differential expression patterns of AKAPs relative to the tumor PAM50 intrinsic subtype, which were most apparent in the basal-like subtype. This pattern was confirmed in primary tumors from TCGA (n = 522) and in a third independent cohort (n = 182). Conclusion Several studies from primary cancers have reported individual AKAP genes to be associated with cancer risk and metastatic relapses as well as direct involvement in cellular invasion and migration processes. Our findings reveal an enrichment of mutations in AKAP genes in metastatic breast cancers and suggest the involvement of AKAPs in the metastatic process. In addition, we report an AKAP gene expression pattern that consistently follows the tumor intrinsic subtype, further suggesting AKAP family members as relevant players in breast cancer biology.
  • Honkela, Antti; Das, Mrinal; Nieminen, Arttu; Dikmen, Onur; Kaski, Samuel (BioMed Central, 2018)
    Abstract Background Users of a personalised recommendation system face a dilemma: recommendations can be improved by learning from data, but only if other users are willing to share their private information. Good personalised predictions are vitally important in precision medicine, but genomic information on which the predictions are based is also particularly sensitive, as it directly identifies the patients and hence cannot easily be anonymised. Differential privacy has emerged as a potentially promising solution: privacy is considered sufficient if presence of individual patients cannot be distinguished. However, differentially private learning with current methods does not improve predictions with feasible data sizes and dimensionalities. Results We show that useful predictors can be learned under powerful differential privacy guarantees, and even from moderately-sized data sets, by demonstrating significant improvements in the accuracy of private drug sensitivity prediction with a new robust private regression method. Our method matches the predictive accuracy of the state-of-the-art non-private lasso regression using only 4x more samples under relatively strong differential privacy guarantees. Good performance with limited data is achieved by limiting the sharing of private information by decreasing the dimensionality and by projecting outliers to fit tighter bounds, therefore needing to add less noise for equal privacy. Conclusions The proposed differentially private regression method combines theoretical appeal and asymptotic efficiency with good prediction accuracy even with moderate-sized data. As already the simple-to-implement method shows promise on the challenging genomic data, we anticipate rapid progress towards practical applications in many fields. Reviewers This article was reviewed by Zoltan Gaspari and David Kreil.
  • Sonntag, Katja; Hashimoto, Hisayoshi; Eyrich, Matthias; Menzel, Moritz; Schubach, Max; Döcker, Dennis; Battke, Florian; Courage, Carolina; Lambertz, Helmut; Handgretinger, Rupert; Biskup, Saskia; Schilbach, Karin (BioMed Central, 2018)
    Abstract Background Cancer vaccines can effectively establish clinically relevant tumor immunity. Novel sequencing approaches rapidly identify the mutational fingerprint of tumors, thus allowing to generate personalized tumor vaccines within a few weeks from diagnosis. Here, we report the case of a 62-year-old patient receiving a four-peptide-vaccine targeting the two sole mutations of his pancreatic tumor, identified via exome sequencing. Methods Vaccination started during chemotherapy in second complete remission and continued monthly thereafter. We tracked IFN-γ+ T cell responses against vaccine peptides in peripheral blood after 12, 17 and 34 vaccinations by analyzing T-cell receptor (TCR) repertoire diversity and epitope-binding regions of peptide-reactive T-cell lines and clones. By restricting analysis to sorted IFN-γ-producing T cells we could assure epitope-specificity, functionality, and TH1 polarization. Results A peptide-specific T-cell response against three of the four vaccine peptides could be detected sequentially. Molecular TCR analysis revealed a broad vaccine-reactive TCR repertoire with clones of discernible specificity. Four identical or convergent TCR sequences could be identified at more than one time-point, indicating timely persistence of vaccine-reactive T cells. One dominant TCR expressing a dual TCRVα chain could be found in three T-cell clones. The observed T-cell responses possibly contributed to clinical outcome: The patient is alive 6 years after initial diagnosis and in complete remission for 4 years now. Conclusions Therapeutic vaccination with a neoantigen-derived four-peptide vaccine resulted in a diverse and long-lasting immune response against these targets which was associated with prolonged clinical remission. These data warrant confirmation in a larger proof-of concept clinical trial.
  • Pöyhönen, Pauli; Kylmälä, Minna; Vesterinen, Paula; Kivistö, Sari; Holmström, Miia; Lauerma, Kirsi; Väänänen, Heikki; Toivonen, Lauri; Hänninen, Helena (BioMed Central, 2018)
    Abstract Background Large myocardial infarction (MI) is associated with adverse left ventricular (LV) remodeling (LVR). We studied the nature of LVR, with specific attention to non-transmural MIs, and the association of peak CK-MB with recovery and chronic phase scar size and LVR. Methods Altogether 41 patients underwent prospectively repeated cardiovascular magnetic resonance at a median of 22 (interquartile range 9–29) days and 10 (8–16) months after the first revascularized MI. Transmural MI was defined as ≥75% enhancement in at least one myocardial segment. Results Peak CK-MB was 86 (40–216) μg/L in median, while recovery and chronic phase scar size were 13 (3–23) % and 8 (2–19) %. Altogether 33 patients (81%) had a non-transmural MI. Peak CK-MB had a strong correlation with recovery and chronic scar size (r ≥ 0.80 for all, r ≥ 0.74 for non-transmural MIs; p < 0.001). Peak CK-MB, recovery scar size, and chronic scar size, were all strongly correlated with chronic wall motion abnormality index (WMAi) (r ≥ 0.75 for all, r ≥ 0.73 for non-transmural MIs; p < 0.001). There was proportional scar size and LV mass resorption of 26% (0–50%) and 6% (− 2–14%) in median. Young age (< 60 years, median) was associated with greater LV mass resorption (median 9%vs.1%, p = 0.007). Conclusions Peak CK-MB has a strong association with chronic scar size and wall motion abnormalities after revascularized non-transmural MI. Considerable infarct resorption happens after the first-month recovery phase. LV mass resorption is related to age, being more common in younger patients.
  • Obscura Acosta, Nidia; Mäkinen, Veli; Tomescu, Alexandru I (BioMed Central, 2018)
    Abstract Background Reconstructing the genome of a species from short fragments is one of the oldest bioinformatics problems. Metagenomic assembly is a variant of the problem asking to reconstruct the circular genomes of all bacterial species present in a sequencing sample. This problem can be naturally formulated as finding a collection of circular walks of a directed graph G that together cover all nodes, or edges, of G. Approach We address this problem with the “safe and complete” framework of Tomescu and Medvedev (Research in computational Molecular biology—20th annual conference, RECOMB 9649:152–163, 2016). An algorithm is called safe if it returns only those walks (also called safe) that appear as subwalk in all metagenomic assembly solutions for G. A safe algorithm is called complete if it returns all safe walks of G. Results We give graph-theoretic characterizations of the safe walks of G, and a safe and complete algorithm finding all safe walks of G. In the node-covering case, our algorithm runs in time $$O(m^2 + n^3)$$ O ( m 2 + n 3 ) , and in the edge-covering case it runs in time $$O(m^2n)$$ O ( m 2 n ) ; n and m denote the number of nodes and edges, respectively, of G. This algorithm constitutes the first theoretical tight upper bound on what can be safely assembled from metagenomic reads using this problem formulation.
  • Lampi, Jussi; Ung-Lanki, Sari; Santalahti, Päivi; Pekkanen, Juha (BioMed Central, 2018)
    Abstract Background Questionnaires can be used to assess perceived indoor air quality and symptoms in schools. Questionnaires for primary school aged children have traditionally been parent-administered, but self-administered questionnaires would be easier to administer and may yield as good, if not better, information. Our aim was to compare the repeatability of self- and parent-administered indoor air questionnaires designed for primary school aged pupils. Methods Indoor air questionnaire with questions on child’s symptoms and perceived indoor air quality in schools was sent to parents of pupils aged 7–12 years in two schools and again after two weeks. Slightly modified version of the questionnaire was administered to pupils aged 9–12 years in another two schools and repeated after a week. 351 (52%) parents and 319 pupils (86%) answered both the first and the second questionnaire. Test-retest repeatability was assessed with intra-class correlation (ICC) and Cohen’s kappa coefficients (k). Results Test-retest repeatability was generally between 0.4–0.7 (ICC; k) in both self- and parent-administered questionnaire. In majority of the questions on symptoms and perceived indoor air quality test-retest repeatability was at the same level or slightly better in self-administered compared to parent-administered questionnaire. Agreement of self- and parent administered questionnaires was generally < 0.4 (ICC; k) in reported symptoms and 0.4–0.6 (ICC; k) in perceived indoor air quality. Conclusions Children aged 9–12 years can give as, or even more, repeatable information about their respiratory symptoms and perceived indoor air quality than their parents. Therefore, it may be possible to use self-administered questionnaires in future studies also with children.
  • Hyytiäinen, Heidi K; Jayaprakash, Balamuralikrishna; Kirjavainen, Pirkka V; Saari, Sampo E; Holopainen, Rauno; Keskinen, Jorma; Hämeri, Kaarle; Hyvärinen, Anne; Boor, Brandon E; Täubel, Martin (BioMed Central, 2018)
    Abstract Background Floor dust is commonly used for microbial determinations in epidemiological studies to estimate early-life indoor microbial exposures. Resuspension of floor dust and its impact on infant microbial exposure is, however, little explored. The aim of our study was to investigate how floor dust resuspension induced by an infant’s crawling motion and an adult walking affects infant inhalation exposure to microbes. Results We conducted controlled chamber experiments with a simplified mechanical crawling infant robot and an adult volunteer walking over carpeted flooring. We applied bacterial 16S rRNA gene sequencing and quantitative PCR to monitor the infant breathing zone microbial content and compared that to the adult breathing zone and the carpet dust as the source. During crawling, fungal and bacterial levels were, on average, 8- to 21-fold higher in the infant breathing zone compared to measurements from the adult breathing zone. During walking experiments, the increase in microbial levels in the infant breathing zone was far less pronounced. The correlation in rank orders of microbial levels in the carpet dust and the corresponding infant breathing zone sample varied between different microbial groups but was mostly moderate. The relative abundance of bacterial taxa was characteristically distinct in carpet dust and infant and adult breathing zones during the infant crawling experiments. Bacterial diversity in carpet dust and the infant breathing zone did not correlate significantly. Conclusions The microbiota in the infant breathing zone differ in absolute quantitative and compositional terms from that of the adult breathing zone and of floor dust. Crawling induces resuspension of floor dust from carpeted flooring, creating a concentrated and localized cloud of microbial content around the infant. Thus, the microbial exposure of infants following dust resuspension is difficult to predict based on common house dust or bulk air measurements. Improved approaches for the assessment of infant microbial exposure, such as sampling at the infant breathing zone level, are needed.
  • Sõritsa, Deniss; Teder, Hindrek; Roosipuu, Retlav; Tamm, Hannes; Laisk-Podar, Triin; Soplepmann, Pille; Altraja, Alan; Salumets, Andres; Peters, Maire (BioMed Central, 2018)
    Abstract Background Benign metastasizing leiomyoma (BML) is an orphan neoplasm commonly characterized by pulmonary metastases consisting of smooth muscle cells. Patients with BML have usually a current or previous uterine leiomyoma, which is therefore suggested to be the most probable source of this tumour. The purpose of this case report was to determine the possible genetic grounds for pulmonary BML. Case presentation We present a case report in an asymptomatic 44-year-old female patient, who has developed uterine leiomyoma with subsequent pulmonary BML. Whole exome sequencing (WES) was used to detect somatic mutations in BML lesion. Somatic single nucleotide mutations were identified by comparing the WES data between the pulmonary metastasis and blood sample of the same BML patient. One heterozygous somatic mutation was selected for validation by Sanger sequencing. Clonality of the pulmonary metastasis and uterine leiomyoma was assessed by X-chromosome inactivation assay. Conclusions We describe a potentially deleterious somatic heterozygous mutation in bone morphogenetic protein 8B (BMP8B) gene (c.1139A > G, Tyr380Cys) that was identified in the pulmonary metastasis and was absent from blood and uterine leiomyoma, and may play a facilitating role in the metastasizing of BML. The clonality assay confirmed a skewed pattern of X-chromosome inactivation, suggesting monoclonal origin of the pulmonary metastases.
  • Pokharel, Kisun; Peippo, Jaana; Honkatukia, Mervi; Seppälä, Arja; Rautiainen, Johanna; Ghanem, Nasser; Hamama, Tuula-Marjatta; Crowe, Mark A; Andersson, Magnus; Li, Meng-Hua; Kantanen, Juha (BioMed Central, 2018)
    Abstract Background The highly prolific breeds of domestic sheep (Ovis aries) are globally valuable genetic resources for sheep industry. Genetic, nutritional and other environmental factors affect prolificacy traits in sheep. To improve our knowledge of the sheep prolificacy traits, we conducted mRNA-miRNA integrated profiling of ovarian tissues from two pure breeds with large (Finnsheep) vs. small (Texel) litter sizes and their F1 crosses, half of which were fed a flushing diet. Results Among the samples, 16,402 genes (60.6% known ovine genes) were expressed, 79 novel miRNAs were found, and a cluster of miRNAs on chromosome 18 was detected. The majority of the differentially expressed genes between breeds were upregulated in the Texel with low prolificacy, owing to the flushing diet effect, whereas a similar pattern was not detected in the Finnsheep. F1 ewes responded similarly to Finnsheep rather than displaying a performance intermediate between the two pure breeds. Conclusions The identification and characterization of differentially expressed genes and miRNAs in the ovaries of sheep provided insights into genetic and environmental factors affecting prolificacy traits. The three genes (CST6, MEPE and HBB) that were differentially expressed between the group of Finnsheep and Texel ewes kept in normal diet appeared to be candidate genes of prolificacy traits and will require further validation.
  • Porter, Charlotte A; Bradley, Kevin M; Hippeläinen, Eero T; Walker, Matthew D; McGowan, Daniel R (Springer Berlin Heidelberg, 2018)
    Abstract Background Post-therapy SPECT/CT imaging of 90Y microspheres delivered to hepatic malignancies is difficult, owing to the continuous, high-energy Bremsstrahlung spectrum emitted by 90Y. This study aimed to evaluate the utility of a commercially available software package (HybridRecon, Hermes Medical Solutions AB) which incorporates full Monte Carlo collimator modelling. Analysis of image quality was performed on both phantom and clinical images in order to ultimately provide a recommendation of an optimum reconstruction for post-therapy 90Y microsphere SPECT/CT imaging. A 3D-printed anthropomorphic liver phantom was filled with 90Y with a sphere-to-background ratio of 4:1 and imaged on a GE Discovery 670 SPECT/CT camera. Datasets were reconstructed using ordered-subsets expectation maximization (OSEM) 1–7 iterations in order to identify the optimal OSEM reconstruction (5 iterations, 15 subsets). Quantitative analysis was subsequently carried out on phantom datasets obtained using four reconstruction algorithms: the default OSEM protocol (2 iterations, 10 subsets) and the optimised OSEM protocol, both with and without full Monte Carlo collimator modelling. The quantitative metrics contrast recovery (CR) and background variability (BV) were calculated. The four algorithms were then used to retrospectively reconstruct 10 selective internal radiation therapy (SIRT) patient datasets which were subsequently blind scored for image quality by a consultant radiologist. Results The optimised OSEM reconstruction (5 iterations, 15 subsets with full MC collimator modelling) increased the CR by 42% (p < 0.001) compared to the default OSEM protocol (2 iterations, 10 subsets). The use of full Monte Carlo collimator modelling was shown to further improve CR by 14% (30 mm sphere, CR = 90%, p < 0.05). The consultant radiologist had a significant preference for the optimised OSEM over the default OSEM protocol (p < 0.001), with the optimised OSEM being the favoured reconstruction in every one of the 10 clinical cases presented. Conclusions OSEM (5 iterations, 15 subsets) with full Monte Carlo collimator modelling is quantitatively the optimal image reconstruction for post-SIRT 90Y Bremsstrahlung SPECT/CT imaging. The use of full Monte Carlo collimator modelling for correction of image-degrading effects significantly increases contrast recovery without degrading clinical image quality.
  • Beenackers, Mariëlle A; Doiron, Dany; Fortier, Isabel; Noordzij, J. Mark; Reinhard, Erica; Courtin, Emilie; Bobak, Martin; Chaix, Basile; Costa, Giuseppe; Dapp, Ulrike; Diez Roux, Ana V; Huisman, Martijn; Grundy, Emily M; Krokstad, Steinar; Martikainen, Pekka; Raina, Parminder; Avendano, Mauricio; van Lenthe, Frank J (BioMed Central, 2018)
    Abstract Background Urbanization and ageing have important implications for public mental health and well-being. Cities pose major challenges for older citizens, but also offer opportunities to develop, test, and implement policies, services, infrastructure, and interventions that promote mental well-being. The MINDMAP project aims to identify the opportunities and challenges posed by urban environmental characteristics for the promotion and management of mental well-being and cognitive function of older individuals. Methods MINDMAP aims to achieve its research objectives by bringing together longitudinal studies from 11 countries covering over 35 cities linked to databases of area-level environmental exposures and social and urban policy indicators. The infrastructure supporting integration of this data will allow multiple MINDMAP investigators to safely and remotely co-analyse individual-level and area-level data. Individual-level data is derived from baseline and follow-up measurements of ten participating cohort studies and provides information on mental well-being outcomes, sociodemographic variables, health behaviour characteristics, social factors, measures of frailty, physical function indicators, and chronic conditions, as well as blood derived clinical biochemistry-based biomarkers and genetic biomarkers. Area-level information on physical environment characteristics (e.g. green spaces, transportation), socioeconomic and sociodemographic characteristics (e.g. neighbourhood income, residential segregation, residential density), and social environment characteristics (e.g. social cohesion, criminality) and national and urban social policies is derived from publically available sources such as geoportals and administrative databases. The linkage, harmonization, and analysis of data from different sources are being carried out using piloted tools to optimize the validity of the research results and transparency of the methodology. Discussion MINDMAP is a novel research collaboration that is combining population-based cohort data with publicly available datasets not typically used for ageing and mental well-being research. Integration of various data sources and observational units into a single platform will help to explain the differences in ageing-related mental and cognitive disorders both within as well as between cities in Europe, the US, Canada, and Russia and to assess the causal pathways and interactions between the urban environment and the individual determinants of mental well-being and cognitive ageing in older adults.