Electrical properties tomography (EPT) is an imaging method that uses a magnetic resonance (MR) system to non-invasively determine the spatial distribution of the conductivity and permittivity of... Show moreElectrical properties tomography (EPT) is an imaging method that uses a magnetic resonance (MR) system to non-invasively determine the spatial distribution of the conductivity and permittivity of the imaged object. This manuscript starts by providing clear definitions about the data required for, and acquired in, EPT, followed by comprehensively formulating the physical equations underlying a large number of analytical EPT techniques. This thorough mathematical overview of EPT harmonizes several EPT techniques in a single type of formulation and gives insight into how they act on the data and what their data requirements are. Furthermore, the review describes machine learning-based algorithms. Matlab code of several differential and iterative integral methods is available upon request. Show less
Leijsen, R.; Berg, C. van den; Webb, A.; Remis, R.; Mandija, S. 2019
Magnetic resonance electrical properties tomography (MR-EPT) is a technique used to estimate the conductivity and permittivity of tissues from MR measurements of the transmit magnetic field.... Show moreMagnetic resonance electrical properties tomography (MR-EPT) is a technique used to estimate the conductivity and permittivity of tissues from MR measurements of the transmit magnetic field. Different reconstruction methods are available; however, all these methods present several limitations, which hamper the clinical applicability. Standard Helmholtz-based MR-EPT methods are severely affected by noise. Iterative reconstruction methods such as contrast source inversion electrical properties tomography (CSI-EPT) are typically time-consuming and are dependent on their initialization. Deep learning (DL) based methods require a large amount of training data before sufficient generalization can be achieved. Here, we investigate the benefits achievable using a hybrid approach, that is, using MR-EPT or DL-EPT as initialization guesses for standard 3D CSI-EPT. Using realistic electromagnetic simulations at 3 and 7 T, the accuracy and precision of hybrid CSI reconstructions are compared with those of standard 3D CSI-EPT reconstructions. Our results indicate that a hybrid method consisting of an initial DL-EPT reconstruction followed by a 3D CSI-EPT reconstruction would be beneficial. DL-EPT combined with standard 3D CSI-EPT exploits the power of data-driven DL-based EPT reconstructions, while the subsequent CSI-EPT facilitates a better generalization by providing data consistency. Show less
Background. The time interval between CRT and surgery in rectal cancer patients is still the subject of debate. The aim of this study was to first evaluate the nationwide use of restaging magnetic... Show moreBackground. The time interval between CRT and surgery in rectal cancer patients is still the subject of debate. The aim of this study was to first evaluate the nationwide use of restaging magnetic resonance imaging (MRI) and its impact on timing of surgery, and, second, to evaluate the impact of timing of surgery after chemoradiotherapy (CRT) on short- and long-term outcomes.Methods. Patients were selected from a collaborative rectal cancer research project including 71 Dutch centres, and were subdivided into two groups according to time interval from the start of preoperative CRT to surgery (< 14 and ae14 weeks).Results. From 2095 registered patients, 475 patients received preoperative CRT. MRI restaging was performed in 79.4% of patients, with a median CRT-MRI interval of 10 weeks (interquartile range [IQR] 8-11) and a median MRI-surgery interval of 4 weeks (IQR 2-5). The CRT-surgery interval groups consisted of 224 (< 14 weeks) and 251 patients (>= 14 weeks), and the long-interval group included a higher proportion of cT4 stage and multivisceral resection patients. Pathological complete response rate (n = 34 [15.2%] vs. n = 47 [18.7%], p = 0.305) and CRM involvement (9.7% vs. 15.9%, p = 0.145) did not significantly differ. Thirty-day surgical complications were similar (20.1% vs. 23.1%, p = 0.943), however no significant differences were found for local and distant recurrence rates, disease-free survival, and overall survival.Conclusions. These real-life data, reflecting routine daily practice in The Netherlands, showed substantial variability in the use and timing of restaging MRI after preoperative CRT for rectal cancer, as well as time interval to surgery. Surgery before or after 14 weeks from the start of CRT resulted in similar short- and long-term outcomes. Show less
Borstlap, W.A.A.; Deijen, C.L.; Dulk, M. den; Bonjer, H.J.; Velde, C.J. van de; Bemelman, W.A.; ... ; Dutch Snapshot Res Grp 2017
Aim A Snapshot study design eliminates changes in treatment and outcome over time. This population based Snapshot study aimed to determine current practice and outcome of rectal cancer treatment... Show moreAim A Snapshot study design eliminates changes in treatment and outcome over time. This population based Snapshot study aimed to determine current practice and outcome of rectal cancer treatment with published landmark randomized controlled trials as a benchmark.Method In this collaborative research project, the dataset of the Dutch Surgical Colorectal Audit was extended with additional treatment and long-term outcome data. All registered patients who underwent resection for rectal cancer in 2011 were eligible. Baseline characteristics and outcome were evaluated against the results of the Dutch TME trial and the COLOR II trial from which the original datasets were obtained.Results A total of 71 hospitals participated, and data were completed for 2102 out of the potential 2633 patients (79.8%). Median follow-up was 41 (interquartile range 25-47) months. Overall circumferential resection margin (CRM) involvement was 9.3% in the Snapshot cohort and 18.5% in the Dutch TME trial. CRM positivity after laparoscopic resection was 7.8% in the Snapshot and 9.5% in the COLOR II trial. Three-year overall local recurrence rate in the Snapshot was 5.9%, with a disease-free survival of 67.1% and overall survival of 79.5%. Benchmarking with the randomized controlled trials revealed an overall favourable long-term outcome of the Snapshot cohort.Conclusion This study showed that current rectal cancer care in a large unselected Dutch population is of high quality, with less positive CRM since the TME trial and oncologically safe implementation of minimally invasive surgery after the COLOR II trial. Show less
Berg, C. van den; Beijersbergen, K.; Nieuwbeerta, P.; Dirkzwager, A. 2017
Empirical literature has revealed that social isolation can affect the rehabilitation of sex offenders after serving their sentence. This process of social isolation can already start during... Show moreEmpirical literature has revealed that social isolation can affect the rehabilitation of sex offenders after serving their sentence. This process of social isolation can already start during incarceration due to strained relationships with fellow prisoners and correctional staff. The current study examined to what extent sex offenders felt socially isolated during incarceration, using survey and registered conviction data on a large sample of male adult prisoners from the Prison Project. It was found that support from and relationships with correctional officers and fellow prisoners were perceived less positive by sex offenders than nonsex offenders. No evidence was found for higher levels of loneliness in sex offenders compared with prisoners convicted for a nonsexual offense. In sum, although the effects were small, sex offenders reported more social isolation during imprisonment compared with nonsex offenders. Show less
Madigan, M.C.; Berg, C. van den; Jager, M.J.; Provis, J.M. 2013
DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To... Show moreDNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants. Show less
