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Matos F, Svensson J, Pavone A, Odstrčil T, Jenko F. Deep learning for Gaussian process soft x-ray tomography model selection in the ASDEX Upgrade tokamak. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:103501. [PMID: 33138591 DOI: 10.1063/5.0020680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Gaussian process tomography (GPT) is a method used for obtaining real-time tomographic reconstructions of the plasma emissivity profile in tokamaks, given some model for the underlying physical processes involved. GPT can also be used, thanks to Bayesian formalism, to perform model selection, i.e., comparing different models and choosing the one with maximum evidence. However, the computations involved in this particular step may become slow for data with high dimensionality, especially when comparing the evidence for many different models. Using measurements collected by the Soft X-Ray (SXR) diagnostic in the ASDEX Upgrade tokamak, we train a convolutional neural network to map SXR tomographic projections to the corresponding GPT model whose evidence is highest. We then compare the network's results, and the time required to calculate them, with those obtained through analytical Bayesian formalism. In addition, we use the network's classifications to produce tomographic reconstructions of the plasma emissivity profile.
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Afghahi MD H, Nasic S, Alhomsi K, Rydell H, Hadimeri H, Svensson J. SAT-268 IN PATIENTS WITH DIABETES AND END STAGE RENAL DISEASE, ASSOCIATION BETWEEN BODY MASS INDEX AND RISK OF MORTALITY IS DIFFERENT IN HEMODIALYSIS AND PERITONEAL DIALYSIS. Kidney Int Rep 2020. [DOI: 10.1016/j.ekir.2020.02.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Tjörnstrand J, Neuman P, Svensson J, Lundin B, Dahlberg LE, Tiderius CJ. Osteoarthritis development related to cartilage quality-the prognostic value of dGEMRIC after anterior cruciate ligament injury. Osteoarthritis Cartilage 2019; 27:1647-1652. [PMID: 31279937 DOI: 10.1016/j.joca.2019.06.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/22/2019] [Accepted: 06/13/2019] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Rupture of the anterior cruciate ligament (ACL) increases the risk of developing osteoarthritis (OA). Delayed Gadolinium enhanced magnetic resonance imaging (MRI) of cartilage (dGEMRIC) investigates cartilage integrity through T1-analysis after intravenous contrast injection. A high dGEMRIC index represents good cartilage quality. The main purpose of this prospective cohort study was to investigate the prognostic value of the dGEMRIC index regarding future knee OA. METHOD 31 patients with ACL injury (mean age 27 ± 6.7 (±SD) years, 19 males) were examined after 2 years with 1.5T dGEMRIC of femoral cartilage. Re-examination 14 years post-injury included weight-bearing knee radiographs, Lysholm and Knee Osteoarthritis Outcome Score (KOOS). RESULTS At the 14-year follow up radiographic OA (ROA) was present in 68% and OA symptoms (SOA) in 42% of the injured knees. The dGEMRIC index of the medial compartment was lower in knees that developed medial ROA, 325 ± 68 (ms±SD) vs 376 ± 47 (51 (7-94)) (difference of means (95% confidence interval (CI))), in patients that developed symptomatic OA (SOA), 327 ± 61 vs 399 ± 42 (52 (11-93)), and poor knee function 337 ± 54 vs 381 ± 52 (48 (7-89)) compared to those that did not develop ROA, SOA or poor function. The dGEMRIC index correlated negatively with the OARSI osteophyte score in medial (r = -0.44, P = 0.01) and lateral (r = -0.38, P = 0.03) compartments. CONCLUSION The associations between a low dGEMRIC index and future ROA, as well as SOA, are in agreement with previous studies and indicate that dGEMRIC has a prognostic value for future knee OA.
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Sörelius K, Svensson J, Matthiessen P, Rutegård J, Rutegård M. A nationwide study on the incidence of mesenteric ischaemia after surgery for rectal cancer demonstrates an association with high arterial ligation. Colorectal Dis 2019; 21:925-931. [PMID: 31062468 DOI: 10.1111/codi.14674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Abstract
AIM The incidence of mesenteric ischaemia after resection for rectal cancer has not been investigated in a population-based setting. The use of high ligation of the inferior mesenteric artery might cause such ischaemia, as the bowel left in situ depends on collateral blood supply after a high tie. METHOD The Swedish Colorectal Cancer Registry was used to identify all patients subjected to an abdominal resection for rectal cancer during the years 2007-2017 inclusive. Mesenteric ischaemia within the first 30 postoperative days was recorded, classified as either stoma necrosis or colonic necrosis. Multivariable logistic regression was used to estimate odds ratios (ORs) with 95% confidence intervals (CIs) for mesenteric ischaemia in relation to high tie, with adjustment for confounding. RESULTS Some 14 657 patients were included, of whom 59 (0.40%) had a reoperation for any type of mesenteric ischaemia, divided into 34 and 25 cases of stoma necrosis and colonic necrosis, respectively. Compared with patients who did not require reoperation for mesenteric ischaemia following rectal cancer surgery, the proportion having high tie was greater (54.2% vs 38.5%; P = 0.032). The adjusted OR for reoperation due to any mesenteric ischaemia with high tie was 2.26 (95% CI 1.34-3.79), while the corresponding estimates for stoma and colonic necrosis, respectively, were 1.60 (95% CI 0.81-3.17) and 3.69 (95% CI 1.57-8.66). CONCLUSION The incidence of reoperation for mesenteric ischaemia after abdominal resection for rectal cancer is low, but the use of a high tie might increase the risk of colonic necrosis demanding surgery.
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Zhang D, König R, Feng Y, Burhenn R, Brezinsek S, Jakubowski M, Buttenschön B, Niemann H, Pavone A, Krychowiak M, Kwak S, Svensson J, Gao Y, Pedersen TS, Alonso A, Baldzuhn J, Beidler CD, Biedermann C, Bozhenkov S, Brunner KJ, Damm H, Hirsch M, Giannone L, Drewelow P, Effenberg F, Fuchert G, Hammond KC, Höfel U, Killer C, Knauer J, Laqua HP, Laube R, Pablant N, Pasch E, Penzel F, Rahbarnia K, Reimold F, Thomsen H, Winters V, Wagner F, Klinger T. First Observation of a Stable Highly Dissipative Divertor Plasma Regime on the Wendelstein 7-X Stellarator. PHYSICAL REVIEW LETTERS 2019; 123:025002. [PMID: 31386539 DOI: 10.1103/physrevlett.123.025002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Indexed: 06/10/2023]
Abstract
For the first time, the optimized stellarator Wendelstein 7-X has operated with an island divertor. An operation regime in hydrogen was found in which the total plasma radiation approached the absorbed heating power without noticeable loss of stored energy. The divertor thermography recorded simultaneously a strong reduction of the heat load on all divertor targets, indicating almost complete power detachment. This operation regime was stably sustained over several energy confinement times until the preprogrammed end of the discharge. The plasma radiation is mainly due to oxygen and is located at the plasma edge. This plasma scenario is reproducible and robust at various heating powers, plasma densities, and gas fueling locations. These experimental results show that the island divertor concept actually works and displays good power dissipation potential, producing a promising exhaust concept for the stellarator reactor line.
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Langenberg A, Svensson J, Marchuk O, Fuchert G, Bozhenkov S, Damm H, Pasch E, Pavone A, Thomsen H, Pablant NA, Burhenn R, Wolf RC. Inference of temperature and density profiles via forward modeling of an x-ray imaging crystal spectrometer within the Minerva Bayesian analysis framework. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:063505. [PMID: 31255024 DOI: 10.1063/1.5086283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
At the Wendelstein 7-X stellarator, the X-ray imaging crystal spectrometer provides line integrated measurements of ion and electron temperatures, plasma flows, as well as impurity densities from a spectroscopic analysis of tracer impurity radiation. In order to infer the actual profiles from line integrated data, a forward modeling approach has been developed within the Minerva Bayesian analysis framework. In this framework, the inversion is realized on the basis of a complete forward model of the diagnostic, including error propagation and utilizing Gaussian processes for generation and inference of arbitrary shaped plasma parameter profiles. For modeling of line integrated data as measured by the detector, the installation geometry of the spectrometer, imaging properties of the crystal, and Gaussian detection noise are considered. The inversion of line integrated data is achieved using the maximum posterior method for plasma parameter profile inference and a Markov chain Monte Carlo sampling of the posterior distribution for calculating uncertainties of the inference process. The inversion method shows a correct and reliable inference of temperature and impurity density profiles from synthesized data within the estimated uncertainties along the whole plasma radius. The application to measured data yields a good match of derived electron temperature profiles to data of the Thomson scattering diagnostic for central electron temperatures between 2 and 5 keV using argon impurities.
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Olsson E, Folkesson E, Peterson P, Önnerfjord P, Tjörnstrand J, Hughes HV, Englund M, Svensson J. Ultra-high field magnetic resonance imaging parameter mapping in the posterior horn of ex vivo human menisci. Osteoarthritis Cartilage 2019; 27:476-483. [PMID: 30552967 PMCID: PMC7610687 DOI: 10.1016/j.joca.2018.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/26/2018] [Accepted: 12/03/2018] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To investigate the relationship between meniscus magnetic resonance (MR) relaxation parameters and meniscus degradation through quantitative imaging of ex vivo posterior horns of menisci from subjects with and without knee osteoarthritis (OA). DESIGN We sampled medial and lateral menisci from ten medial compartment knee OA patients (mean age 63 years) undergoing total knee replacement and from ten deceased donors (references, mean age 51 years). MR relaxation parameters T2*, T2 and T1 of the posterior horn were measured at a 9.4 T scanner. Comparisons were made between OA patients and references (with adjustment for age) as well as between medial and lateral menisci from the same knees. RESULTS Mean values (standard deviation) of mean T2* were 13 (3.8), 6.9 (2.3), 7.2 (1.9) and 7.2 (1.7) ms for the medial and lateral patient menisci and the medial and lateral reference menisci, respectively. Corresponding values were 17 (3.7), 9.0 (2.2), 12 (4) and 9.0 (1.3) ms for T2 and 1810 (150), 1630 (30), 1580 (90) and 1560 (50) ms for T1. All three relaxation times were significantly longer in medial OA menisci compared to the other groups. Among medial reference menisci, relaxation times (mainly T1) tended to increase with age. CONCLUSIONS MR relaxation times T2*, T2 and T1 in the posterior horn are longer in the medial menisci of patients with end-stage medial compartment knee OA compared to the corresponding lateral menisci and to reference menisci. The meniscus seems to undergo intrasubstance alterations related to both OA and ageing.
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Linderholm BK, Ekholm M, Wännstig AK, Lundstedt D, Carlsson L, Tzikas AK, Svensson J, Kristiansson H, Filges S, Ståhlberg A. Abstract P1-16-09: Low-dose chemotherapy (CT) + bevacizumab (Bev) combined with unchanged endocrine treatment (ET) in patients with recurrent luminal breast cancer progressing during ET – Effect determined by standard imaging and changes in ctDNA and CTC during treatment. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p1-16-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Several mechanisms are involved in the development of endocrine resistance, such as mutations in the ESR1, PIK3CA, and TP53 genes and/or up-regulation of tyrosine kinase receptors such as the endothelial growth factor (VEGF) receptor. Preclinical data have revealed that sensitivity to endocrine therapy may be restored if these pathways are blocked.
Aims: To investigate the progression-free survival (PFS), overall response rate (ORR), and the toxicity of the study treatment. To use circulating tumor cells (CTC) and circulating tumor DNA (ct-DNA) at base-line and during treatment for next generation sequencing (NGS) to investigate whether changes in tumor mutations or in levels of CTC/ct-DNA correlate to treatment efficacy.
Patients and methods: Thirty-two patients aged 46-77 years with confirmed advanced breast cancer (ABC) progressing during ET were included. Treatment consisted of unchanged ET with the addition of cyclophosphamide 50mg x 1 and capecitabine 500mg x 3 daily + bevacizumab 15mg/kg iv. every third week (q21). Blood samples for analysis of CTC and ctDNA were collected at base-line, after the 1st and 2nd course, and at progression. CTC were isolated by use of an immune-magnetic selection (ADNA-test) and sequenced by NGS. ctDNA were analysed by the SiMSen-Seq (Simple Multiplexed PCR-based barcoding of DNA for Sensitive mutation detection using Sequencing) that allows mutant frequencies < 0.1% to be detected.
Results: One patient did not start treatment and 2 were not evaluable. Palliative chemotherapy (1-2 lines) had been delivered before inclusion to 28% and > 1 line of palliative ET to 58% of the patients. A total of 72% (n=21) of the patients had visceral disease (of whom 7 had liver metastases), and 28% (n=8) patients bone-only disease. Median PFS was 9.1 months (range 2.1-59.3 months). Best responses were: 1 patient (3%) received complete remission; 7 patients (24%) partial response; 16 patients (55%) SD (of whom 12 had CB, defined as SD > 24 weeks), and 5 (17%) had progressive disease. The ORR (defined as CR, PR, or CB) was 69%. The most common toxicity was hypertension (62%), that resulted in termination in 2 patients, and 1 patient stopped treatment due to thrombocytopenia. Other side-effects were proteinuria grade 1-3 (24%); hand-foot-syndrome grade 1-2 (45%); mucositis grade 1 (14%); nausea grade 1 (14%) and diarrhea grade 1-3 (10%). CTC was isolated in 12 patients (37%). Three out of the 5 patients with PD at 12 weeks had detectable CTCs at base-line. Base-line ESR1, PIK3CA and TP53 mutations were found in CTC from 2 patients (17%), 7 patients (58%), and 5 patients (42%), respectively, but did not correlate to response.
Conclusion: The treatment was well tolerated with an ORR of 69%, which is considered very good in this setting. CTCs were only isolated in 37% of the patients which is comparable to previously reported results in metastatic luminal breast cancer and thus not a feasible method for monitoring treatment effect. Results on levels of consecutive ctDNA, as well as mutation pattern in relation treatment effect will be presented.
Citation Format: Linderholm BK, Ekholm M, Wännstig A-K, Lundstedt D, Carlsson L, Tzikas A-K, Svensson J, Kristiansson H, Filges S, Ståhlberg A. Low-dose chemotherapy (CT) + bevacizumab (Bev) combined with unchanged endocrine treatment (ET) in patients with recurrent luminal breast cancer progressing during ET – Effect determined by standard imaging and changes in ctDNA and CTC during treatment [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-16-09.
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Birkebaek NH, Kahlert J, Bjarnason R, Drivvoll AK, Johansen A, Konradsdottir E, Pundziute-Lyckå A, Samuelsson U, Skrivarhaug T, Svensson J. Body mass index standard deviation score and obesity in children with type 1 diabetes in the Nordic countries. HbA 1c and other predictors of increasing BMISDS. Pediatr Diabetes 2018; 19:1198-1205. [PMID: 29781227 DOI: 10.1111/pedi.12693] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 03/30/2018] [Accepted: 04/30/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Intensified insulin therapy may increase body weight and cause obesity. This study compared body mass index standard deviation score (BMISDS) and obesity rate in children with type 1 diabetes (T1D) in Denmark, Iceland, Norway and Sweden, and uncovered predictors for increasing BMISDS. METHODS Data registered in the Nordic national childhood diabetes databases during the period 2008-2012 on children below 15 years with T1D for more than 3 months were compiled, including information on gender, age, diabetes duration, hemoglobin A1c (HbA1c ), insulin dose, severe hypoglycemia (SH), treatment modality, height and weight. The Swedish reference chart for BMI was used for calculating BMISDS. RESULTS Totally, 11 025 children (48% females) (30 994 registrations) were included. Medians by the last recorded examination were: age, 13.5 years; diabetes duration, 4.3 years; HbA1c , 7.9% (63 mmol/mol); insulin dose, 0.8 IU/kg/d and BMISDS, 0.70. Obesity rate was 18.5%. Adjusted mean BMISDS (BMISDS adj) was inversely related to HbA1c and directly to diabetes duration. Higher BMISDS adj was found in those with an insulin dose above 0.6 IU/kg/d, and in girls above 10 years. Pump users had higher BMISDS adj than pen users, and patients with registered SH had higher BMISDS adj than patients without SH (both P < .001). CONCLUSION Obesity rate in children with T1D in the Nordic countries is high, however, with country differences. Low HbA1c , long diabetes duration, higher insulin dose, pump treatment and experiencing a SH predicted higher BMISDS. Diabetes caregivers should balance the risk of obesity and the benefit of a very low HbA1c.
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Langenberg A, Pablant NA, Wegner T, Traverso P, Marchuk O, Bräuer T, Geiger B, Fuchert G, Bozhenkov S, Pasch E, Grulke O, Kunkel F, Killer C, Nicolai D, Satheeswaran G, Hollfeld KP, Schweer B, Krings T, Drews P, Offermanns G, Pavone A, Svensson J, Alonso JA, Burhenn R, Wolf RC. Prospects of X-ray imaging spectrometers for impurity transport: Recent results from the stellarator Wendelstein 7-X (invited). THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:10G101. [PMID: 30399890 DOI: 10.1063/1.5036536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Abstract
This paper reports on the design and the performance of the recently upgraded X-ray imaging spectrometer systems, X-ray imaging crystal spectrometer and high resolution X-ray imaging spectrometer, installed at the optimized stellarator Wendelstein 7-X. High resolution spectra of highly ionized, He-like Si, Ar, Ti, and Fe as well as H-like Ar have been observed. A cross comparison of ion and electron temperature profiles derived from a spectral fit and tomographic inversion of Ar and Fe spectra shows a reasonable match with both the spectrometers. The also measured impurity density profiles of Ar and Fe have peaked densities at radial positions that are in qualitative agreement with the expectations from the He-like impurity fractional abundances, given the measured temperature profiles. Repeated measurements of impurity decay times have been demonstrated with an accuracy of 1 ms via injection of non-recycling Ti, Fe, and Mo impurities using a laser blow-off system.
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Fredheim S, Foli-Andersen P, Laerkholm G, Svensson J, Juhl CB, Olsen B, Pilgaard K, Johannesen J. Adrenaline and cortisol levels are lower during nighttime than daytime hypoglycaemia in children with type 1 diabetes. Acta Paediatr 2018. [PMID: 29520851 DOI: 10.1111/apa.14310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AIM We investigated children's counter regulatory hormone profiles during a hyperinsulinaemic hypoglycaemic clamp procedure at day and night. METHODS In 2013, we assessed the counter regulatory response to hypoglycaemia in eight outpatients with type 1 diabetes, recruited from the Herlev Hospital, Denmark, at a mean age of 9.6 ± 2.3 years. Hyperinsulinaemic 80 mU/m2 /min clamps were performed with a stepwise reduction in plasma glucose from euglycaemia (7-9 mmol/L) to hypoglycaemia (<3.5 mmol/L) and the glucose nadir (≤2.2 mmol/L) during the day and night. Adrenaline, cortisol, glucagon and growth hormone levels were assessed. RESULTS Adrenaline and growth hormone levels were higher during the day versus the night (p = 0.04 and p = 0.01, respectively). However, at the glucose nadir, the level of adrenaline was lower during the night than the day (0.6 ± 0.2 versus 1.9 ± 0.5 nmol/L, p = 0.016) and cortisol was lower during the day than the night (42 ± 15 versus 319 ± 81 nmol/L, p = 0.016). No differences were demonstrated for glucagon and growth hormone levels based on the same criteria. CONCLUSION The adrenaline response was blunted during nocturnal iatrogenic hypoglycaemia in our study cohort, and no increase in cortisol levels was demonstrated.
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Wang T, Mazon D, Svensson J, Li D, Jardin A, Verdoolaege G. Incorporating magnetic equilibrium information in Gaussian process tomography for soft X-ray spectroscopy at WEST. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:10F103. [PMID: 30399849 DOI: 10.1063/1.5039152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/14/2018] [Indexed: 06/08/2023]
Abstract
Gaussian process tomography (GPT) [J. Svensson, JET Internal Report EFDA-JET-PR(11)24, 2011 and D. Li, J. Svensson, H. Thomsen, F. Medina, A. Werner, and R. Wolf, Rev. Sci. Instrum. 84, 083506 (2013)] is a recently developed tomography method applied earlier to soft X-ray (SXR) spectroscopy on WEST-Tungsten (W) Environment in Steady-state Tokamak. The short execution time of the algorithm makes GPT an important candidate for providing real-time information on impurity transport and for fast MHD control. In earlier work, GPT has shown its flexibility by providing good reconstruction results without background information about the magnetic equilibrium. On the other hand, information about the magnetic flux surface geometry can in general be useful for additional regularization of the solution. In this paper, we develop a way to take into account the equilibrium information, by constructing a covariance matrix of the prior Gaussian process depending on the flux surface geometry. The GPT method is validated using synthetic SXR emissivity profiles relevant to WEST plasmas and compares favorably with the classical algorithm based on minimization of the Fisher information.
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Pavone A, Svensson J, Langenberg A, Pablant N, Hoefel U, Kwak S, Wolf RC. Bayesian uncertainty calculation in neural network inference of ion and electron temperature profiles at W7-X. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:10K102. [PMID: 30399785 DOI: 10.1063/1.5039286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
We make use of a Bayesian description of the neural network (NN) training for the calculation of the uncertainties in the NN prediction. Having uncertainties on the NN prediction allows having a quantitative measure for trusting the NN outcome and comparing it with other methods. Within the Bayesian framework, the uncertainties can be calculated under different approximations. The NN has been trained with the purpose of inferring ion and electron temperature profile from measurements of a X-ray imaging diagnostic at W7-X. The NN has been trained in such a way that it constitutes an approximation of a full Bayesian model of the diagnostic, implemented within the Minerva framework. The network has been evaluated using measured data and the uncertainties calculated under different approximations have been compared with each other, finding that neglecting the noise on the NN input can lead to an underestimation of the error bar magnitude in the range of 10%-30%.
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He S, Blombäck M, Boström F, Wallen H, Svensson J, Östlund A. An increased tendency in fibrinogen activity and its association with a hypo-fibrinolytic state in early stages after injury in patients without acute traumatic coagulopathy (ATC). J Thromb Thrombolysis 2018; 45:477-485. [PMID: 29564685 PMCID: PMC5889778 DOI: 10.1007/s11239-018-1642-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acute traumatic coagulopathy (ATC) diagnosed by prolongation of APTT and/or PT/INR involves alterations in platelet activity, coagulation and fibrinolysis. However, data showing the haemostatic situation in injured patients without ATC are scarce. To assess whether haemostatic impairment is also present in injured patients without ATC, ten injured patients without ATC and ten normal individuals were examined. The patients were sampled on arrival at the emergency department 0, 2, 12 h after surgical or other intervention. Thrombin generation, fibrin formation and fibrin proteolysis were determined via several laboratory methods, using tissue factor as the coagulation trigger. Thrombograms demonstrated that trauma accelerated both thrombin generation and decay. In the presence of unaffected peak thrombin levels, these two contradictory effects cancelled each other out, leading to the global endogenous thrombin potential (ETP) remaining normal. Under the mediation of normal ETP, fibrin network permeability (Ks) kept the reference levels in the two groups of subjects. Fibrinogen (FBG) activity (Clauss) rose with time from 0 to 2 h and 12 h, which significantly slowed down Clot Lysis Potential as determined by an in vitro method with exogenous t-PA. Summary: the main haemostatic impairment in the present patients concerned an increased tendency in FBG activity. Since an increase in FBG is a biomarker of acute inflammation and also predicts greater fibrin production which down-regulates fibrinolysis, we suggest that during early stages after injury, patients without ATC may suffer from worsening inflammation and confront enhancement of thrombosis risk due to dysfunction of fibrinolysis.
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Wang T, Mazon D, Svensson J, Li D, Jardin A, Verdoolaege G. Gaussian process tomography for soft x-ray spectroscopy at WEST without equilibrium information. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:063505. [PMID: 29960552 DOI: 10.1063/1.5023162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Gaussian process tomography (GPT) is a recently developed tomography method based on the Bayesian probability theory [J. Svensson, JET Internal Report EFDA-JET-PR(11)24, 2011 and Li et al., Rev. Sci. Instrum. 84, 083506 (2013)]. By modeling the soft X-ray (SXR) emissivity field in a poloidal cross section as a Gaussian process, the Bayesian SXR tomography can be carried out in a robust and extremely fast way. Owing to the short execution time of the algorithm, GPT is an important candidate for providing real-time reconstructions with a view to impurity transport and fast magnetohydrodynamic control. In addition, the Bayesian formalism allows quantifying uncertainty on the inferred parameters. In this paper, the GPT technique is validated using a synthetic data set expected from the WEST tokamak, and the results are shown of its application to the reconstruction of SXR emissivity profiles measured on Tore Supra. The method is compared with the standard algorithm based on minimization of the Fisher information.
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Thorsen SU, Pipper CB, Johannesen J, Mortensen HB, Pociot F, Svensson J. '25-Hydroxyvitamin D, Autoantigenic and Total Antibody Concentrations: Results from a Danish Case-control Study of Newly Diagnosed Patients with Childhood Type 1 Diabetes and their Healthy Siblings'. Scand J Immunol 2017; 87:46-53. [PMID: 29125655 DOI: 10.1111/sji.12632] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 11/05/2017] [Indexed: 01/03/2023]
Abstract
B cells have recently entered the stage as an important accessory player in type 1 diabetes (T1D) etiopathogenesis. Experimental studies suggest regulatory functions of vitamin D on B cells. However, only a few human studies, with considerable methodological limitations, have been conducted within this field. Our objective was to investigate whether higher 25-hydroxyvitamin D (25(OH)D) concentrations were inversely associated with β-cell autoantigens glutamic acid decarboxylase (isoform 65) (GADA) and insulinoma-associated antigen-2A (IA-2A). Further, we also wanted to examine the relationship between 25(OH)D and total antibody concentrations. We randomly selected 500 patients with newly diagnosed T1D and 500 siblings for 25(OH)D, antibody and genetic analysis from the population-based Danish Registry of Childhood and Adolescent Diabetes. The relative change (RC) in the mean concentration of GADA, IA-2A and antibody isotypes by a 10 nmol/l increase in 25(OH)D concentration was modelled by a robust log-normal regression model. We found no association between 25(OH)D and GADA [adjusted RC per 10 nmol/l increase: 1.00; 95% confidence interval (CI): 0.98-1.02] and IA-2A [adjusted RC per 10 nmol/l increase: 0.92; CI: 0.76-1.12]. Further, 25(OH)D was not associated with the total concentration of antibody isotypes [immunoglobulin (Ig)A, IgE, IgG and IgM]. All null findings were unaltered after adjustment for genetic variation in the vitamin D pathway. Physiological concentrations of 25(OH)D are unlikely to have a clinically important effect on antibody concentrations in a paediatric population of newly diagnosed patients with T1D and their healthy siblings.
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Arshad SA, Cordey JG, McDonald DC, Farthing J, Joffrin E, Hellermann MV, Roach CM, Svensson J. Chapter 11: Data Validation, Analysis, and Applications for Fusion Plasmas. FUSION SCIENCE AND TECHNOLOGY 2017. [DOI: 10.13182/fst08-a1683] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Langenberg A, Svensson J, Thomsen H, Marchuk O, Pablant NA, Burhenn R, Wolf RC. Forward Modeling of X-Ray Imaging Crystal Spectrometers Within the Minerva Bayesian Analysis Framework. FUSION SCIENCE AND TECHNOLOGY 2017. [DOI: 10.13182/fst15-181] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Sandahl K, Nielsen LB, Svensson J, Johannesen J, Pociot F, Mortensen HB, Hougaard P, Broe R, Rasmussen ML, Grauslund J, Peto T, Olsen BS. Increased mortality in a Danish cohort of young people with Type 1 diabetes mellitus followed for 24 years. Diabet Med 2017; 34:380-386. [PMID: 27027777 DOI: 10.1111/dme.13124] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/29/2016] [Indexed: 11/28/2022]
Abstract
AIM To determine the mortality rate in a Danish cohort of children and adolescents diagnosed with Type 1 diabetes mellitus compared with the general population. METHODS In 1987 and 1989 we included 884 children and 1020 adolescents aged 20 years and under, corresponding to 75% of all Danish children and adolescents with Type 1 diabetes, in two nationwide studies in Denmark. Those who had participated in both investigations (n = 720) were followed until 1 January 2014, using the Danish Civil Registration System on death certificates and emigration. We derived the expected number of deaths in the cohort, using population data values from Statistics Denmark to calculate the standardized mortality ratio. Survival analysis was performed using Cox proportional hazards model. RESULTS During the 24 years of follow-up, 49 (6.8%) patients died, resulting in a standardized mortality ratio of 4.8 (95% confidence interval 3.5, 6.2) compared with the age-standardized general population. A 1% increase in baseline HbA1c (1989), available in 718 of 720 patients, was associated with all-cause mortality (hazard ratio = 1.38; 95% confidence interval 1.2, 1.6; P < 0.0001). Type 1 diabetes with multiple complications was the most common reported cause of death (36.7%). CONCLUSION We found an increased mortality rate in this cohort of children and adolescents with Type 1 diabetes compared with the general population. The only predictor for increased risk of death up to 24 years after inclusion was the HbA1c level in 1989. This emphasizes the importance of achieving optimal metabolic control in young people with Type 1 diabetes.
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Moen F, Svensson J, Steen Carlsson K. Assessing the value of cancer treatments from real world data—Issues, empirical examples and lessons learnt. J Cancer Policy 2017. [DOI: 10.1016/j.jcpo.2016.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Timpka J, Svensson J, Nilsson MH, Pålhagen S, Hagell P, Odin P. Workforce unavailability in Parkinson's disease. Acta Neurol Scand 2017; 135:332-338. [PMID: 27072284 DOI: 10.1111/ane.12602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2016] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Individuals with Parkinson's disease (PD) become unavailable in the workforce earlier than comparable members of the general population. This may result in significant social insurance expenses, but as workforce participation can be a source for social interaction and a vital part of the personal identity, there are likely to be personal implications extending far beyond the economic aspects. This study aimed to identify aspects that may contribute to workforce unavailability in people with PD. MATERIALS & METHODS This was a cross-sectional registry study using data from the Swedish national quality registry for PD and included persons with PD in Skåne County, Sweden who were younger than 65 years. Variables were selected from the registry based on earlier studies and clinical experience and were tested for association with unavailability in the workforce: first in a series of simple regression analyses and then in a multiple logistic regression analysis. RESULTS A total of 99 persons with PD-of whom 59 were available and 40 were unavailable in the workforce-were included in the study. Age (OR per year: 1.47, 95% CI: 1.18-1.85; P < 0.01) and anxiety (OR: 6.81, 95% CI: 1.20-38.67; P = 0.03) were significant contributing factors for unavailability in the workforce. CONCLUSIONS Based on the findings in this exploratory study, anxiety-a potentially modifiable factor-and age may be contributing factors for workforce unavailability in PD. However, prospective studies are warranted to confirm the findings and the causation of the association between anxiety and workforce unavailability needs to be clarified.
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Birkebaek NH, Drivvoll AK, Aakeson K, Bjarnason R, Johansen A, Samuelsson U, Skrivarhaug T, Thorsson AV, Svensson J. Incidence of severe hypoglycemia in children with type 1 diabetes in the Nordic countries in the period 2008-2012: association with hemoglobin A 1c and treatment modality. BMJ Open Diabetes Res Care 2017; 5:e000377. [PMID: 28761652 PMCID: PMC5530237 DOI: 10.1136/bmjdrc-2016-000377] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/11/2017] [Accepted: 04/17/2017] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Treatment of type 1 diabetes has been intensified aiming at normalizing blood glucose, which may increase the risk of severe hypoglycemia (SH). We aimed to compare the incidence of SH events in the four Nordic countries Denmark, Iceland, Norway and Sweden, and to assess the influence of hemoglobin A1c (HbA1c) and treatment modalities on the frequency of SH; particularly, to explore if a HbA1c target ≤6.7% (50 mmol/mol) is feasible. RESEARCH DESIGN AND METHODS Data on children below 15 years with a diabetes duration more than 1 year, registered in the national childhood diabetes databases in the four Nordic countries from 2008 to 2012, were compiled. Data completeness was more than 95%. RESULTS Totally 8806 (48% females) patients with 29 715 person years were included, mean age and diabetes duration were 11 years and 5.1 years, respectively. The overall rate of SH was 6.0 per 100 patient-years, and did not change during the study period. The Swedish population constantly had the lowest SH incidence while it decreased significantly in the Danish population. HbA1c decreased significantly over time (p<0.01), while the number of pump users increased (p<0.01). Stratifying for HbA1c levels showed the lowest risk of SH in patients with HbA1c ≤6.7% (≤50 mmol/mol), but in the statistical models adjusting for possible confounders the difference between the HbA1c groups disappeared. Pump users had the lowest SH risk, also after adjusting for possible confounders. CONCLUSIONS Risk of SH differs between the Nordic countries with the lowest risk in Sweden. Pump therapy was associated with decreased risk of SH. The low HbA1c group had the same or a lower risk of SH compared with the highest HbA1c groups. A target HbA1c ≤6.7% (≤50 mmol/mol) seems achievable without increasing the risk of SH.
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Paterson RW, Heywood WE, Heslegrave AJ, Magdalinou NK, Andreasson U, Sirka E, Bliss E, Slattery CF, Toombs J, Svensson J, Johansson P, Fox NC, Zetterberg H, Mills K, Schott JM. A targeted proteomic multiplex CSF assay identifies increased malate dehydrogenase and other neurodegenerative biomarkers in individuals with Alzheimer's disease pathology. Transl Psychiatry 2016; 6:e952. [PMID: 27845782 PMCID: PMC5314115 DOI: 10.1038/tp.2016.194] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/31/2016] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia. Biomarkers are required to identify individuals in the preclinical phase, explain phenotypic diversity, measure progression and estimate prognosis. The development of assays to validate candidate biomarkers is costly and time-consuming. Targeted proteomics is an attractive means of quantifying novel proteins in cerebrospinal and other fluids, and has potential to help overcome this bottleneck in biomarker development. We used a previously validated multiplexed 10-min, targeted proteomic assay to assess 54 candidate cerebrospinal fluid (CSF) biomarkers in two independent cohorts comprising individuals with neurodegenerative dementias and healthy controls. Individuals were classified as 'AD' or 'non-AD' on the basis of their CSF T-tau and amyloid Aβ1-42 profile measured using enzyme-linked immunosorbent assay; biomarkers of interest were compared using univariate and multivariate analyses. In all, 35/31 individuals in Cohort 1 and 46/36 in Cohort 2 fulfilled criteria for AD/non-AD profile CSF, respectively. After adjustment for multiple comparisons, five proteins were elevated significantly in AD CSF compared with non-AD CSF in both cohorts: malate dehydrogenase; total APOE; chitinase-3-like protein 1 (YKL-40); osteopontin and cystatin C. In an independent multivariate orthogonal projection to latent structures discriminant analysis (OPLS-DA), these proteins were also identified as major contributors to the separation between AD and non-AD in both cohorts. Independent of CSF Aβ1-42 and tau, a combination of these biomarkers differentiated AD and non-AD with an area under curve (AUC)=0.88. This targeted proteomic multiple reaction monitoring (MRM)-based assay can simultaneously and rapidly measure multiple candidate CSF biomarkers. Applying this technique to AD we demonstrate differences in proteins involved in glucose metabolism and neuroinflammation that collectively have potential clinical diagnostic utility.
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Krychowiak M, Adnan A, Alonso A, Andreeva T, Baldzuhn J, Barbui T, Beurskens M, Biel W, Biedermann C, Blackwell BD, Bosch HS, Bozhenkov S, Brakel R, Bräuer T, Brotas de Carvalho B, Burhenn R, Buttenschön B, Cappa A, Cseh G, Czarnecka A, Dinklage A, Drews P, Dzikowicka A, Effenberg F, Endler M, Erckmann V, Estrada T, Ford O, Fornal T, Frerichs H, Fuchert G, Geiger J, Grulke O, Harris JH, Hartfuß HJ, Hartmann D, Hathiramani D, Hirsch M, Höfel U, Jabłoński S, Jakubowski MW, Kaczmarczyk J, Klinger T, Klose S, Knauer J, Kocsis G, König R, Kornejew P, Krämer-Flecken A, Krawczyk N, Kremeyer T, Książek I, Kubkowska M, Langenberg A, Laqua HP, Laux M, Lazerson S, Liang Y, Liu SC, Lorenz A, Marchuk AO, Marsen S, Moncada V, Naujoks D, Neilson H, Neubauer O, Neuner U, Niemann H, Oosterbeek JW, Otte M, Pablant N, Pasch E, Sunn Pedersen T, Pisano F, Rahbarnia K, Ryć L, Schmitz O, Schmuck S, Schneider W, Schröder T, Schuhmacher H, Schweer B, Standley B, Stange T, Stephey L, Svensson J, Szabolics T, Szepesi T, Thomsen H, Travere JM, Trimino Mora H, Tsuchiya H, Weir GM, Wenzel U, Werner A, Wiegel B, Windisch T, Wolf R, Wurden GA, Zhang D, Zimbal A, Zoletnik S. Overview of diagnostic performance and results for the first operation phase in Wendelstein 7-X (invited). THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:11D304. [PMID: 27910389 DOI: 10.1063/1.4964376] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Wendelstein 7-X, a superconducting optimized stellarator built in Greifswald/Germany, started its first plasmas with the last closed flux surface (LCFS) defined by 5 uncooled graphite limiters in December 2015. At the end of the 10 weeks long experimental campaign (OP1.1) more than 20 independent diagnostic systems were in operation, allowing detailed studies of many interesting plasma phenomena. For example, fast neutral gas manometers supported by video cameras (including one fast-frame camera with frame rates of tens of kHz) as well as visible cameras with different interference filters, with field of views covering all ten half-modules of the stellarator, discovered a MARFE-like radiation zone on the inboard side of machine module 4. This structure is presumably triggered by an inadvertent plasma-wall interaction in module 4 resulting in a high impurity influx that terminates some discharges by radiation cooling. The main plasma parameters achieved in OP1.1 exceeded predicted values in discharges of a length reaching 6 s. Although OP1.1 is characterized by short pulses, many of the diagnostics are already designed for quasi-steady state operation of 30 min discharges heated at 10 MW of ECRH. An overview of diagnostic performance for OP1.1 is given, including some highlights from the physics campaigns.
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Andersen AJB, Ostenfeld A, Pipper CB, Olsen BS, Hertz AM, Jørgensen LK, Høgsmose J, Svensson J. Optimum bolus wizard settings in insulin pumps in children with Type 1 diabetes. Diabet Med 2016; 33:1360-5. [PMID: 26773826 DOI: 10.1111/dme.13064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/11/2016] [Indexed: 10/22/2022]
Abstract
AIM To evaluate current insulin pump settings in an optimally regulated paediatric population using bolus wizard. METHODS We used a retrospective study design to analyse data from 124 children on insulin pump therapy who had optimum HbA1c levels [< 59 mmol/mol (< 7.5%)] and no history of severe hypoglycaemic events. Bolus wizard settings were used to calculate the insulin to carbohydrate factors and insulin sensitivity factors. Multiple regression analysis was used to analyse the variables associated with the calculation factors. RESULTS Insulin to carbohydrate factor varied from 276 in the youngest group to 424 in the oldest group, and increased according to age. Insulin sensitivity factor was highest in the group aged 6 to < 12 years, with a value of 125. Age, amount of carbohydrates, number of boluses per day and insulin per kg were all significantly associated with both calculation factors. Furthermore, duration of insulin pump treatment was significantly associated with insulin sensitivity factor and percentage bolus/basal was significantly associated with insulin to carbohydrate factor. Gender, diabetes duration and BMI were not associated with any of the calculation factors. CONCLUSION Optimum insulin pump settings at pump initiation depend on both insulin requirements and use of the pump. Settings need to be individualized because the standardized calculation factors are not constant for children. There is a need to develop specific age- and insulin dose-dependent calculation factors.
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