34 results on '"Belien J"'
Search Results
2. Dose optimization in high-dose-rate brachytherapy: A literature review of quantitative models from 1990 to 2010
- Author
-
De Boeck, L., Beliën, J., and Egyed, W.
- Published
- 2014
- Full Text
- View/download PDF
3. There is no increased risk for colorectal cancer and adenomas in patients with diverticulitis: a retrospective longitudinal study
- Author
-
Lam, T. J., Meurs-Szojda, M. M., Gundlach, L., Belien, J. A. M., Meijer, G. A., Mulder, C. J., and Felt-Bersma, R. J. F.
- Published
- 2010
- Full Text
- View/download PDF
4. Next Generation Sequencing in health care and clinical research: attuning all steps
- Author
-
Rigter, T., Belien, J. A. M., de Wert, G. M. W. R., Ploem, C., Bunnik, E. M., Bredenoord, A. L., Cornel, M. C., Human genetics, Pathology, CCA - Cancer biology and immunology, APH - Quality of Care, APH - Personalized Medicine, and Amsterdam Reproduction & Development (AR&D)
- Published
- 2019
5. Image analysis in clinical pathology
- Author
-
Meijer, G A, Belien, J A M, van Diest, P J, and Baak, J P A
- Published
- 1997
6. Rapidly progressive amyotrophic lateral sclerosis is associated with microglial reactivity and small heat shock protein expression in reactive astrocytes
- Author
-
Gorter, R. P., primary, Stephenson, J., additional, Nutma, E., additional, Anink, J., additional, de Jonge, J. C., additional, Baron, W., additional, Jahreiβ, M.‐C., additional, Belien, J. A. M., additional, van Noort, J. M., additional, Mijnsbergen, C., additional, Aronica, E., additional, and Amor, S., additional
- Published
- 2018
- Full Text
- View/download PDF
7. European Study on OR/MS Education: Preliminary Insight into relations with the Labour Market
- Author
-
Belien, J., Ittmann, H., Laumanns, M., Miranda, J.L., Pato, M.V., and Teixeira, A.P.
- Abstract
Introduction In line with the recent developments in OR/MS Education, a survey (available at https://ec.europa.eu/eusurvey/runner/ORMSeducation) was conducted amongst European universities and other higher education institutions (HEIs) from June to October 2015. The survey and related activities correspond to the first phase of the European Study on OR/MS Education. The purpose of the study is to obtain detailed insight into the current state of this field in Europe. The study was supported by the Association of European Operational Research Societies (EURO). It should be noted that EURO currently includes 31 member countries. Most of these member societies are from Europe but three countries, outside of the European continent, namely Israel, South Africa and Tunisia are also EURO member societies. A few of the survey respondents identified their affiliation in European countries that are not represented in EURO (e.g., Ukraine), or stated that they are visiting fellows from abroad (e.g., India); in this regard the terms Europe and European, as used in this article, shall include these respondents., This study was made possible through the kind support of EURO, a significant number of OR societies in EURO, collaborating colleagues, the EU-Survey services from the European Commission, and Springer Verlag. We acknowledge and thank them for that.
- Published
- 2016
- Full Text
- View/download PDF
8. European Study on OR/MS Education: first results and prospects
- Author
-
Belien, J., Ittmann, H., Laumanns, M., Miranda, J.L., Pato, M., and Teixeira, A.P.
- Abstract
Introduction Education in Operational Research / Management Science (OR/MS) has shown significant progress, but further developments that may help to identify key factors related to OR/MS programmes at Higher Education Institutions (HEI) are still required. With the support of partner institutions of the Association of European Operational Research Societies (EURO), a study on OR/MS education in European countries was initiated. The first phase focused on the following main aspects namely: enrolment of students to OR/MS courses, first year OR/MS students’ failure rates, continuous promotion of the subject area, OR/MS courses, and the transition of graduates into the labour market. With this objective, the working group prepared a questionnaire aimed mainly at the OR/MS academic community, in order to gain a better understanding of how HEI - universities, colleges, polytechnics and research centers - are addressing OR/MS education topics in Europe., This study was made possible through the kind support of EURO, a significant number of OR societies in EURO, collaborating colleagues, the EU-Survey services from the European Commission, and Springer Verlag. We acknowledge and thank them for that.
- Published
- 2016
- Full Text
- View/download PDF
9. Rapidly progressive amyotrophic lateral sclerosis is associated with microglial reactivity and small heat shock protein expression in reactive astrocytes.
- Author
-
Gorter, R. P., Stephenson, J., Nutma, E., Anink, J., Jonge, J. C., Baron, W., Jahreiβ, M.‐C., Belien, J. A. M., Noort, J. M., Mijnsbergen, C., Aronica, E., and Amor, S.
- Subjects
AMYOTROPHIC lateral sclerosis ,MOTOR neurons ,HEAT shock proteins ,PROTEIN expression ,NEUROGLIA ,SPINAL cord ,MUSCLE weakness - Abstract
Aims: Amyotrophic lateral sclerosis (ALS) is a chronic neurodegenerative disease characterized by progressive loss of motor neurons, muscle weakness, spasticity, paralysis and death usually within 2–5 years of onset. Neuroinflammation is a hallmark of ALS pathology characterized by activation of glial cells, which respond by upregulating small heat shock proteins (HSPBs), but the exact underlying pathological mechanisms are still largely unknown. Here, we investigated the association between ALS disease duration, lower motor neuron loss, TARDNA‐binding protein 43 (TDP‐43) pathology, neuroinflammation and HSPB expression. Methods: With immunohistochemistry, we examined HSPB1, HSPB5, HSPB6, HSPB8 and HSP16.2 expression in cervical, thoracic and sacral spinal cord regions in 12 ALS cases, seven with short disease duration (SDD), five with moderate disease duration (MDD), and ten age‐matched controls. Expression was quantified using ImageJ to examine HSP expression, motor neuron numbers, microglial and astrocyte density and phosphorylated TDP‐43 (pTDP‐43+) inclusions. Results: SDD was associated with elevated HSPB5 and 8 expression in lateral tract astrocytes, while HSP16.2 expression was increased in astrocytes in MDD cases. SDD cases had higher numbers of motor neurons and microglial activation than MDD cases, but similar levels of motor neurons with pTDP‐43+ inclusions. Conclusions: Increased expression of several HSPBs in lateral column astrocytes suggests that astrocytes play a role in the pathogenesis of ALS. SDD is associated with increased microgliosis, HSPB5 and 8 expression in astrocytes, and only minor changes in motor neuron loss. This suggests that the interaction between motor neurons, microglia and astrocytes determines neuronal fate and functional decline in ALS. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
10. DNA quantitation of distal bile duct carcinoma measured by image and flow cytometry
- Author
-
Rijken, A. M., Belien, J. A., van Gulik, T. M., Polak, M. M., Offerhaus, G. J., Gouma, D. J., Baak, J. P., Pathology, CCA - Cancer immunology, CCA - Biomarkers, AII - Cancer immunology, and Other departments
- Subjects
embryonic structures - Abstract
OBJECTIVE: To evaluate discrepancies between flow cytometry (FCM) and image cytometry (ICM), ploidy incidence and relation between DNA ploidies and survival in distal bile duct carcinomas (DBDCs).STUDY DESIGN: Forty-four archival tumor samples from patients with DBDC who underwent subtotal pancreatoduodenectomy from 1985 to 1996 were examined for DNA ploidy using FCM and ICM.RESULTS: Overall, 59% (26/44) of the tumors were aneuploid by at least one of the two techniques. We detected more cases of aneuploidy with ICM than FCM in formalin-fixed, paraffin-embedded DBDCs, 62% (21/34) versus 33% (13/40), respectively. When results could be compared, moderate strength of agreement (kappa = .45) was demonstrated. No correlation was found between DNA ploidy by FCM, ICM or combined FCM-ICM and survival time (P = .80, P = .35, and P = .54, respectively).CONCLUSION: Approximately 59% of DNA histograms contained aneuploid cell populations. Although ICM, as compared to FCM, is more sensitive in assessing the ploidy status of DBDC, both methods were complementary. Most discrepancies between FCM and ICM were due to the dilution of aneuploid populations by non-neoplastic diploid cells. DNA ploidy assessment in DBDC did not offer the possibility of improving the ability to predict survival.
- Published
- 1999
11. Erratum:Counting mitoses by image processing in Feulgen stained breast cancer sections: The influence of resolution (Cytometry (1997) 28:2)
- Author
-
Belien, J. A.M., Baak, J. P.A., Van Diest, P. J., and Van Ginkel, A. H.M.
- Published
- 1997
- Full Text
- View/download PDF
12. HPV testing on self collected cervicovaginal lavage specimens as screening method for women who do not attend cervical screening: cohort study
- Author
-
Gok, M., primary, Heideman, D. A M, additional, van Kemenade, F. J, additional, Berkhof, J., additional, Rozendaal, L., additional, Spruyt, J. W M, additional, Voorhorst, F., additional, Belien, J. A M, additional, Babovic, M., additional, Snijders, P. J F, additional, and Meijer, C. J L M, additional
- Published
- 2010
- Full Text
- View/download PDF
13. A method for counting mitoses by image processing in Feulgen stained breast cancer sections
- Author
-
ten Kate, T.K., Belien, J., Smeulders, A.W.M., Baak, J.P.A., and IVI (FNWI)
- Subjects
sense organs - Published
- 1993
14. Gross genomic damage measured by DNA image cytometry independently predicts gastric cancer patient survival
- Author
-
Belien, J A M, primary, Buffart, T E, additional, Gill, A J, additional, Broeckaert, M A M, additional, Quirke, P, additional, Meijer, G A, additional, and Grabsch, H I, additional
- Published
- 2009
- Full Text
- View/download PDF
15. There is no increased risk for colorectal cancer and adenomas in patients with diverticulitis: a retrospective longitudinal study
- Author
-
Lam, T. J., primary, Meurs-Szojda, M. M., additional, Gundlach, L., additional, Belien, J. A. M., additional, Meijer, G. A., additional, Mulder, C. J., additional, and Felt-Bersma, R. J. F., additional
- Published
- 2009
- Full Text
- View/download PDF
16. Combined assessment of EGFR pathway-related molecular markers and prognosis of NSCLC patients
- Author
-
Ruiz, M I Galleges, primary, Floor, K, additional, Steinberg, S M, additional, Grünberg, K, additional, Thunnissen, F B J M, additional, Belien, J A M, additional, Meijer, G A, additional, Peters, G J, additional, Smit, E F, additional, Rodriguez, J A, additional, and Giaccone, G, additional
- Published
- 2008
- Full Text
- View/download PDF
17. An expert system for histological typing and grading of invasive breast cancer. First set up
- Author
-
van Diest, P J, Belien, J A, Baak, J P, Pathology, CCA - Cancer immunology, CCA - Biomarkers, and AII - Cancer immunology
- Abstract
This article describes the set up of a rule-based expert system for histologic typing and grading of invasive breast cancer, which is designed to be a user-friendly tool that may be helpful for teaching and to support diagnosis making. The system raises questions and offers fixed choices to the user (usually yes/no) until a histologic diagnosis can be made with reasonable probability or enough data are available to assign a grade. As to histologic typing, the expert system is able to make the following diagnoses: ductal carcinoma, lobular carcinoma, medullary carcinoma, colloidal carcinoma, tubular carcinoma, and invasive cribriform carcinoma. If the diagnosis "ductal carcinoma" is arrived, the system offers the option to assign a histologic grade to the lesion. A first evaluation of the system in 30 cases (five each of the different subtypes) with unequivocal diagnoses by two human experts showed that the system classified 29 of the tumours in the same way as the human experts. The discrepancy case was solved after adding one rule to the system. Ten cases where a discrepancy existed between the original diagnosis of a referring centre and a reviewing human expert were all classified by the expert system in the same way as the human expert. The expert system thus seems to perform well. Further plans for evaluating, modifying and expanding the system are disclosed.
- Published
- 1992
- Full Text
- View/download PDF
18. Corrigendum to “Dose optimization in high-dose-rate brachytherapy: A literature review of quantitative models from 1990–2010” [ORHC 3 (2) (2014) 80–90]
- Author
-
De Boeck, L., Beliën, J., and Egyed, W.
- Published
- 2014
- Full Text
- View/download PDF
19. Fully automated microvessel counting and hot spot selection by image processing of whole tumour sections in invasive breast cancer
- Author
-
Belien, J. A., primary, Somi, S., additional, de Jong, J. S., additional, van Diest, P. J., additional, and Baak, J. P., additional
- Published
- 1999
- Full Text
- View/download PDF
20. Progression from colorectal adenoma to carcinoma is associated with non- random chromosomal gains as detected by comparative genomic hybridisation
- Author
-
Meijer, G. A., primary, Hermsen, M. A., additional, Baak, J. P., additional, van Diest, P. J., additional, Meuwissen, S. G., additional, Belien, J. A., additional, Hoovers, J. M., additional, Joenje, H., additional, Snijders, P. J., additional, and Walboomers, J. M., additional
- Published
- 1998
- Full Text
- View/download PDF
21. Origins of ... image analysis in clinical pathology.
- Author
-
Meijer, G A, primary, Belien, J A, additional, van Diest, P J, additional, and Baak, J P, additional
- Published
- 1997
- Full Text
- View/download PDF
22. Drug Resistance-Associated Marker Lrp for Prediction of Response to Chemotherapy and Prognoses in Advanced Ovarian Carcinoma
- Author
-
lzquierdo, M. A., primary, Zee, A. G. J.v. d., additional, Vermorken, J. B., additional, Valk, P. v. d., additional, Belien, J. A. M., additional, Giaccone, G., additional, Scheffer, G. L., additional, Flens, M. J., additional, Pinedo, H. M., additional, Kenemans, P., additional, Meijer, C. J. L. M., additional, Vries, E. G. E.d., additional, and Scheper, R. J., additional
- Published
- 1995
- Full Text
- View/download PDF
23. Combined assessment of EGFR pathway-related molecular markers and prognosis of NSCLC patients.
- Author
-
Ruiz, M. I. Galleges, Floor, K., Steinberg, S. M., Grünberg, K., Thunnissen, F. B. J. M., Belien, J. A. M., Meijer, G. A., Peters, G. J., Smit, E. F., Rodriguez, J. A., Giaccone, G., Galleges Ruiz, M I, and Grünberg, K
- Subjects
BIOMARKERS ,EPIDERMAL growth factor ,CANCER patients ,GENETIC mutation ,TUMORS ,CYTOKINES ,IMMUNOHISTOCHEMISTRY ,SMALL cell lung cancer - Abstract
The purpose of this study is to evaluate the prognostic value of the combined assessment of multiple molecular markers related to the epidermal growth factor receptor (EGFR) pathway in resected non-small cell lung cancer (NSCLC) patients. Tumour specimens of 178 NSCLC patients were collected and analysed for EGFR and KRAS mutation status by DNA sequencing, and for EGFR copy number by fluorescent in situ hybridisation. Tissue microarrays were generated and used to determine the expression of multiple EGFR pathway-related proteins by immunohistochemistry. We analysed the association between each marker and patient prognosis. Univariate analyses for each clinical variable and each molecular marker were performed using Kaplan-Meier curves and log-rank tests. From these results, we selected the variables KRAS mutations and expression of cytoplasmic EGFR, granular pERK, nuclear pSTAT3, cytoplasmic E-cadherin and cytoplasmic pCMET to enter into a Cox proportional hazards model, along with stage as the strongest clinical variable related with prognosis. Of the EGFR-related markers evaluated here, the markers EGFR, pERK, pSTAT3, E-cadherin, pCMET and mutations in KRAS were associated with survival when analysed in combination in our patient cohort, with P=0.00015 as the P-value for a test of the additional impact of markers on prognosis, after taking stage into consideration. Confirmation of the impact of these markers in independent studies will be necessary. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
24. Optimization approaches for recyclable municipal solid waste collection : Optimalisatiemethodes voor inzameling van recycleerbaar huishoudelijk afval
- Author
-
Van Engeland, J, Belien, J, Eyckmans, J, De Boeck, L, and De Jaeger, S
- Abstract
Waste management or rather materials management is an important policy subject. Residents, legislators and planners are confronted with ever increasing targets for reused or recycled material flows. In this thesis, the focus is on the design of collection schemes for recyclable municipal solid waste. The toolbox offered by the field of combinatorial optimization is used to find optimal or near-optimal solutions for these waste collection problems. After a thorough review on the literature on strategic network optimization models in waste reverse supply chains, two real-life waste collection problems are considered. The first one is about the collection of recyclables from households on a tactical level. The second one concerns the collection of containers from civic amenity sites and is situated on a tactical-operational level. The models aim at minimizing the total cost, which consists of vehicle and personnel costs. Both problems prove hard to solve. Since a general purpose solver could not find satisfactory results, alternative solution approaches, based on a problem decomposition, are proposed. A mixed integer linear programming based heuristic, combined with a column generation lower bound procedure gives good results for the first problem. For the container collection problem however, two alternative approaches are developed. A first one is a cutting plane heuristic based on combinatorial Benders decomposition. A second one applies a route generation and route selection scheme. At least for the problem instances considered in this thesis, the latter outperforms the former. Therefore, the route generation and selection solution process is embedded in an optimization-simulation model. This model incorporates, next to cost, also environmental impacts in its objective function. Additionally, the solutions are simulated to evaluate their behavior under real-life conditions. status: published
- Published
- 2019
25. Design of integrated scheduling and simulation models to optimize people flows and maximise safety. : Ontwerp van geïntegreerde plannings- en simulatiemodellen voor het optimaliseren van mensenstromen en het maximaliseren van veiligheid
- Author
-
Vermuyten, H, Wauters, T, Reniers, G, De Boeck, L, and Belien, J
- Abstract
The study of pedestrian walking behaviour and crowd dynamics is an important topic with many applications. Many computationally efficient but less accurate macroscopic models (where the crowd is described as a whole using average quantities such as density and velocity at a certain location and time) and computationally less efficient but more accurate microscopic models (where each pedestrian is described as a separate entity) have been developed to describe the walking behaviour of individual pedestrians and large crowds. Moreover, many optimisation models have been proposed to solve problems involving pedestrians. Most of these models have hitherto focused on evacuation problems, where for a given building and an initial distribution of pedestrians, the optimal evacuation plan for each pedestrian is computed. A few researchers have also focused on design problems to find the optimal layout of a pedestrian facility or bottleneck passages. In this thesis, we consider the link between timetabling problems and crowd flow optimisation. Indeed, the assignment of events to timeslots and rooms in a timetable has an impact on the resulting people flows. For example, in a university course timetable, at the end of each timeslot, students have to switch rooms to go to their next class. This can cause congestion problems in the halls and stairwells in universities where the class rooms are concentrated in one or a few buildings. Furthermore, if the building needs to be evacuated at a certain time, this evacuation process is also influenced by the university course timetable. After all, the timetable determines how many people are present in the building in each timeslot and in which rooms. University course timetables are not the only example. The timetable at large conferences, music festivals, cultural events, or sports events also determines the people flows during the event. This thesis consists of four main parts. Chapter 2 presents a review of optimisation models for pedestrian evacuation and design problems. Relevant empirical research and descriptive (mathematical) models of pedestrian walking behaviour are also discussed. This review shows that most models include the inverse relationship between density and walking speed, but that calibration and implementation of the proposed models are lacking. Chapter 3 focuses on the university course timetabling problem (UCTP) at KU Leuven Campus Brussels. A two-stage mixed-integer programming (MIP) approach is developed to build a timetable that maximises the scheduling preferences and minimises the travel times of students between lectures in consecutive timeslots. Pedestrians are modelled using a macroscopic network model with a density-dependent arc traverse time. The model is extended to optimise evacuations time of students in the event of an emergency. Computational results show that the model succeeds in constructing timetables with reduced travel or egress times. However, the model fails to solve large real-life instances, such as the KU Leuven instance. Therefore, a heuristic approach is developed to solve the problem. In contrast to the two-stage MIP approach, the heuristic is able to find good quality solutions for the KU Leuven instance. Moreover, it succeeds in improving upon the solutions found by the two-stage MIP approach for all other test instances. In Chapter 4, we develop a generic, flexible model for timetabling incorporating resulting people flows. To keep the model generic and tractable, only the assignment of events to rooms is optimised, while the assignment of events to timeslots is considered given. The pedestrian walking behaviour and crowd dynamics are described using the microscopic pedestrian simulator Menge developed by Curtis et al. (2016). A surrogate-based tabu search heuristic is proposed to solve the problem. The surrogate model is used to speed up the search by filtering the number of candidate solutions that are evaluated using the expensive Menge simulator. The performance of different surrogate models is evaluated. The model is used to solve two applications, one where we minimise evacuation times and one where we minimise travel times between events in consecutive timeslots. The results show that for both applications the model succeeds in building timetables with significantly reduced travel or egress times. Finally, the model is implemented in a scheduling tool with graphical user interface and applied to the room assignment problem at KU Leuven Campus Brussels. It shows that our model is able to tackle real-life problem instances with large numbers of pedestrians. Finally, Chapter 5 compares the network model of Chapter 3 and the microscopic Menge simulator of Chapter 4. Using exhaustive search on small problem instances, the quality assigned to each solution in the solution space by the different models is compared in detail. Moreover, the modelling power and the robustness of the models with respect to the calibration of their parameters is discussed. ispartof: pages:529-530 nrpages: 2 status: published
- Published
- 2019
26. Collaborative shipping: an analysis of can-order replenishment policies, cost-sharing agreements, and information distortion. : Collaborative shipping: an analysis of can-order replenishment policies, cost-sharing agreements, and information distortion
- Author
-
Padilla Tinoco, S, Belien, J, and Boute, R
- Abstract
This dissertation analyzes the stochastic multi-item inventory problem from the horizontal collaboration point of view. In Chapter 2 of this dissertation, we cover the general features of the Joint replenishment problem (JRP), and we classify the existing JRP models according to the demand characteristics. The resulting categorizations provide a useful overview for researchers studying inventory replenishment problems, by providing detailed information on the inventory system characteristics and the employed solution approaches, highlighting articles that involve stochastic variables (e.g., demand arrivals or lead times) and present exact solution approaches. Further, a description of the most commonly used allocation mechanisms is presented together with their formulation. In Chapter 3, we present a Continuous-Time Markov Chain (CTMC) model to compute the steady-state distribution of the possible state transitions of the two-company setting when orders are synchronized using the can-order policy. The CTMC model allows us to quantify the exact inventory and transportation cost performance of each company in the collaboration, and to optimize the optimal control parameters of the can-order policy that maximizes the coalition gains, i.e., minimizes the total joint logistics costs. Once the collaboration costs are calculated, two decisions have to be made: (i) which set of costs will be redistributed, and (ii) how those costs will be allocated. We consider different agreements to distribute the costs (or gains) of the collaboration, ranging from no cost redistribution at all, sharing the transportation costs (or its gains) only, to sharing the total logistics costs (or its gains) that are impacted by the collaboration. Also, we study four different allocation mechanisms to redistribute the collaboration costs/gains. Each of these allocation mechanisms can be applied to each of the four sets of costs. We quantify the individual cost performance of transportation and inventory holdings, and we investigate which cost-sharing agreement enables a long-term partnership where each company obtains individual gains when they set up a collaborative shipping agreement. While Chapter 3 studies the performance of the collaboration under the can-order policy and the long-term stability per type of cost-sharing agreement, Chapter 4 focusses on the non-cooperative framework of the information game. We investigate the incentives for information distortion and whether/when this may pose a threat to the stability (and thus the long-term viability) of the collaboration. Specifically, we investigate the best reporting strategy for each company, assuming that each company works out by reasoning. That is, a company may misreport its demand in order to maximize its realized individual gains on the assumption that the other company behaves in equal manner. Of course, the resulting realized individual gains depend on the specific set of costs to be redistributed and on the allocation mechanism selected. Further, we investigate two types of contract to allocate the costs among the companies. We employ the concept of dominance, i.e., by iteratively eliminating dominated strategies, to find the best reporting strategy under each cost-sharing agreement and to analyze under which settings truth-telling reporting may be an equilibrium. In the inventory management literature, the lot size of the replenishment orders is usually determined by the retailer to balance the fixed cost per order against the holding costs, whereby the transportation utilization rate or the CO2 implications are not considered. In Chapter 5 we revise the stand-alone and collaborative inventory models taking sustainability concerns into account. We thus reformulate for both models the classical single objective optimization approach as a multi-objective inventory problem. Conceptually, we investigate the individual costs and the total carbon emissions generated as the result of the storage of each inventory item, and the frequencies of individual (and joint) orders placed. We make use of a non-dominated sorting procedure to eliminate all possible dominated combinations of control parameters of the can-order policy, i.e., combinations that result in a higher carbon emission for a given cost, in order to identify the set of efficient solutions (Pareto optimal solutions). These results are used to provide some insights about the effectiveness of different ordering policies to control carbon emissions. The results of the multi-criteria decision analysis indicates that a slight percentage cost increase results in a significant reduction of carbon emissions. Finally, Chapter 6 summarizes the conclusions, addresses the limitations of this dissertation, and suggests avenues for further research by highlighting both trends and gaps in the research field. status: published
- Published
- 2018
27. The 1+Million Genomes Minimal Dataset for Cancer.
- Author
-
Riba M, Sala C, Culhane AC, Flobak Å, Patocs A, Boye K, Plevova K, Pospíšilová Š, Gandolfi G, Morelli MJ, Bucci G, Edsjö A, Lassen U, Al-Shahrour F, Lopez-Bigas N, Hovland R, Cuppen E, Valencia A, Poirel HA, Rosenquist R, Scollen S, Arenas Marquez J, Belien J, De Nicolo A, De Maria R, Torrents D, and Tonon G
- Subjects
- Humans, Genomics methods, Databases, Genetic, Neoplasms genetics, Genome, Human
- Published
- 2024
- Full Text
- View/download PDF
28. Hypertrophic and keloid scars fail to progress from the CD34 - /α-smooth muscle actin (α-SMA) + immature scar phenotype and show gradient differences in α-SMA and p16 expression.
- Author
-
Limandjaja GC, Belien JM, Scheper RJ, Niessen FB, and Gibbs S
- Subjects
- Actins, Humans, Muscle, Smooth pathology, Phenotype, Cicatrix, Hypertrophic pathology, Keloid pathology
- Abstract
Background: Our understanding of the pathogenesis underlying keloid scar formation is still very limited, and the morphological distinction between hypertrophic and keloid scars remains difficult., Objectives: To test whether hypertrophic and keloid scars may reflect an inability to progress from immaturity to the desired mature normotrophic scar phenotype., Methods: Using whole-biopsy imaging and an objectively quantifiable way to analyse immunoreactivity, we have compared the immunohistopathological profiles of young immature scars with mature normotrophic scars, hypertrophic scars, and keloids with their surrounding-normal-skin., Results: Abnormal scars (hypertrophic scars and keloids) maintain the immature scar phenotype, characterized by a CD34
- (tumour biomarker) and α-smooth muscle actin (α-SMA)+ (myofibroblast) dermal region. This is in contrast to normal skin, surrounding-normal-skin and mature normotrophic scars that were CD34+ / α-SMA- . Immature, hypertrophic and keloid scars showed abnormal epidermal differentiation (involucrin), but only hypertrophic scars and keloids showed increased epidermal thickness. Immature scars did show increased epidermal and dermal proliferation (Ki67), which was absent from abnormal scars, where mesenchymal hypercellularity (vimentin) and senescence (p16) were predominant. Keloidal collagen and α-SMA were previously considered to distinguish between hypertrophic scars and keloids. However, α-SMA staining was present in both abnormal scar types, while keloidal collagen was present mostly in keloids. There were no obvious signs of heterogeneity within keloid scars, and the surrounding-normal-skin resembled normal skin., Conclusions: Both abnormal scar types showed a unique CD34- /α-SMA+ /p16+ scar phenotype, but the differences between hypertrophic scars and keloids observed in this study were of a gradient rather than absolute nature. This suggests that scar progression to the mature normal scar phenotype is, for as yet unknown reasons, hindered in hypertrophic and keloid scars. What's already known about this topic? Hypertrophic and keloid scars both have sustained epidermal barrier dysfunction, suggesting the persistence of an immature scar phenotype. Morphological distinction between hypertrophic and keloid scars remains a topic of debate, although α-smooth muscle actin (α-SMA) and keloidal collagen have been considered distinguishing features of hypertrophic and keloid scars, respectively. It has been suggested that keloids are not simply homogeneous growths, as heterogeneity within keloid scars and possible involvement of the surrounding-normal-skin have been reported. What does this study add? An extensive whole-biopsy imaging and quantifiable immunohistochemical assessment of immature, mature normal, hypertrophic and keloid scars, including normal skin surrounding keloids. Hypertrophic and keloid scars maintain dermal characteristics of immature scars, rather than transitioning into the normal mature phenotype. Differences between hypertrophic and keloid scars were of a gradient rather than absolute nature, with keloids showing the more extreme phenotype. There was no obvious heterogeneity within keloids, and the normal skin surrounding keloids resembled normal skin. What is the translational message? Keloids remain primarily a clinical diagnosis. A raised scar with the CD34- /α-SMA+ /p16+ phenotype with strong immunoreactivity for p16 and significant amounts of keloidal collagen, together with a thickened and strongly abnormal involucrin-stained epidermis, would sway the diagnosis towards keloid scars. A hypertrophic scar seems more likely when the CD34- /α-SMA+ /p16+ phenotype shows very strong presence of α-SMA+ in large dermal nodules, with lesser p16 staining and absent or negligible keloidal collagen., (© 2019 The Authors. British Journal of Dermatology published by John Wiley & Sons Ltd on behalf of British Association of Dermatologists.)- Published
- 2020
- Full Text
- View/download PDF
29. Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.
- Author
-
Zhang C, Bijlard J, Staiger C, Scollen S, van Enckevort D, Hoogstrate Y, Senf A, Hiltemann S, Repo S, Pipping W, Bierkens M, Payralbe S, Stringer B, Heringa J, Stubbs A, Bonino Da Silva Santos LO, Belien J, Weistra W, Azevedo R, van Bochove K, Meijer G, Boiten JW, Rambla J, Fijneman R, Spalding JD, and Abeln S
- Abstract
The availability of high-throughput molecular profiling techniques has provided more accurate and informative data for regular clinical studies. Nevertheless, complex computational workflows are required to interpret these data. Over the past years, the data volume has been growing explosively, requiring robust human data management to organise and integrate the data efficiently. For this reason, we set up an ELIXIR implementation study, together with the Translational research IT (TraIT) programme, to design a data ecosystem that is able to link raw and interpreted data. In this project, the data from the TraIT Cell Line Use Case (TraIT-CLUC) are used as a test case for this system. Within this ecosystem, we use the European Genome-phenome Archive (EGA) to store raw molecular profiling data; tranSMART to collect interpreted molecular profiling data and clinical data for corresponding samples; and Galaxy to store, run and manage the computational workflows. We can integrate these data by linking their repositories systematically. To showcase our design, we have structured the TraIT-CLUC data, which contain a variety of molecular profiling data types, for storage in both tranSMART and EGA. The metadata provided allows referencing between tranSMART and EGA, fulfilling the cycle of data submission and discovery; we have also designed a data flow from EGA to Galaxy, enabling reanalysis of the raw data in Galaxy. In this way, users can select patient cohorts in tranSMART, trace them back to the raw data and perform (re)analysis in Galaxy. Our conclusion is that the majority of metadata does not necessarily need to be stored (redundantly) in both databases, but that instead FAIR persistent identifiers should be available for well-defined data ontology levels: study, data access committee, physical sample, data sample and raw data file. This approach will pave the way for the stable linkage and reuse of data., Competing Interests: Competing interests: No competing interests were disclosed.
- Published
- 2017
- Full Text
- View/download PDF
30. DNA ploidy measurement in oral leukoplakia: different results between flow and image cytometry.
- Author
-
Brouns ER, Bloemena E, Belien JA, Broeckaert MA, Aartman IH, and van der Waal I
- Subjects
- Adult, Aged, Female, Humans, Male, Middle Aged, Reproducibility of Results, Retrospective Studies, Aneuploidy, DNA, Neoplasm genetics, Flow Cytometry methods, Image Cytometry methods, Leukoplakia, Oral genetics
- Abstract
The estimated prevalence of oral leukoplakia is worldwide approximately 2%, with an annual malignant transformation rate of approximately 1%. The aim of the present study was to evaluate the possible contribution of ploidy measurement to the prediction of the clinical course, in a well defined cohort of patients with oral leukoplakia. Ploidy was measured by both flow cytometry (FCM-DNA) and image cytometry (ICM-DNA) and we focussed on the comparison of the two different techniques to determine ploidy. A total of 41 patients have been included, with a mean age of 59 years (range 36-78 years). With FCM-DNA, three lesions were aneuploid, with ICM-DNA, 19 lesions were aneuploid. DNA ploidy was compared with clinicopathological and patients parameters. There were no statistically significant differences between DNA ploidy and any patient factor with both FCM-DNA and ICM-DNA. Using FCM-DNA, DNA aneuploid lesions showed statistically significant more dysplasia (p=0.04) than diploid lesions. Furthermore, DNA aneuploid lesions were more frequently encountered at high-risk locations (p=0.03) as being determined with FCM-DNA. These relations were not found when DNA ploidy was determined with ICM-DNA., (Copyright © 2012 Elsevier Ltd. All rights reserved.)
- Published
- 2012
- Full Text
- View/download PDF
31. Up-regulation of gene expression by hypoxia is mediated predominantly by hypoxia-inducible factor 1 (HIF-1).
- Author
-
Greijer AE, van der Groep P, Kemming D, Shvarts A, Semenza GL, Meijer GA, van de Wiel MA, Belien JA, van Diest PJ, and van der Wall E
- Subjects
- Animals, Apoptosis genetics, Cell Movement genetics, Cytoskeleton genetics, DNA Repair genetics, DNA-Directed DNA Polymerase genetics, Down-Regulation genetics, Galactokinase genetics, Galectin 3 genetics, Gelsolin genetics, Gene Expression Profiling methods, Glucose Transporter Type 1, Glycolysis genetics, Hypoxia-Inducible Factor 1, Hypoxia-Inducible Factor 1, alpha Subunit, Membrane Proteins genetics, Mice, Monosaccharide Transport Proteins genetics, Oligonucleotide Array Sequence Analysis methods, Proto-Oncogene Proteins genetics, RNA, Messenger genetics, rhoA GTP-Binding Protein genetics, DNA-Binding Proteins genetics, Fibroblasts physiology, Hypoxia genetics, Nuclear Proteins genetics, Transcription Factors genetics, Up-Regulation genetics
- Abstract
The hypoxia-inducible factor 1 (HIF-1) plays a critical role in cellular responses to hypoxia. The aim of the present study was to evaluate which genes are induced by hypoxia, and whether this induction is mediated by HIF-1, by expression microarray analysis of wt and HIF-1alpha null mouse fibroblasts. Forty-five genes were up-regulated by hypoxia and 40 (89%) of these were regulated by HIF-1. Of the 114 genes down-regulated by hypoxia, 19 (17%) were HIF-1-dependent. All glycolytic enzymes were strongly up-regulated by hypoxia in a HIF-1-dependent manner. Genes already known to be related to hypoxia, such as glucose transporter 1, BNIP3, and hypoxia-induced gene 1, were induced. In addition, multiple new HIF-1-regulated genes were identified, including genes involved in metabolism (adenylate kinase 4, galactokinase), apoptosis (galectin-3 and gelsolin), and invasion (RhoA). Genes down-regulated by hypoxia were involved in cytoskeleton maintenance (Rho kinase), mRNA processing (heterogeneous nuclear ribonucleoprotein H1 and splicing factor), and DNA repair (REV3). Furthermore, seven cDNAs from genes with unknown function or expressed sequence tags (ESTs) were up-regulated and 27 such cDNAs were down-regulated. In conclusion, hypoxia causes down- rather than up-regulation of gene expression and HIF-1 seems to play a major role in the regulation of hypoxia-induced genes., (Copyright 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.)
- Published
- 2005
- Full Text
- View/download PDF
32. DNA quantitation of distal bile duct carcinoma measured by image and flow cytometry.
- Author
-
Rijken AM, Belien JA, van Gulik TM, Polak MM, Offerhaus GJ, Gouma DJ, and Baak JP
- Subjects
- Adult, Aged, Bile Duct Neoplasms mortality, Bile Duct Neoplasms pathology, Carcinoma mortality, Carcinoma pathology, Cell Nucleus genetics, Cell Nucleus pathology, Female, Humans, Karyometry, Male, Middle Aged, Pancreaticoduodenectomy, Ploidies, Survival Rate, Bile Duct Neoplasms genetics, Carcinoma genetics, DNA, Neoplasm analysis, Flow Cytometry methods, Image Cytometry methods
- Abstract
Objective: To evaluate discrepancies between flow cytometry (FCM) and image cytometry (ICM), ploidy incidence and relation between DNA ploidies and survival in distal bile duct carcinomas (DBDCs)., Study Design: Forty-four archival tumor samples from patients with DBDC who underwent subtotal pancreatoduodenectomy from 1985 to 1996 were examined for DNA ploidy using FCM and ICM., Results: Overall, 59% (26/44) of the tumors were aneuploid by at least one of the two techniques. We detected more cases of aneuploidy with ICM than FCM in formalin-fixed, paraffin-embedded DBDCs, 62% (21/34) versus 33% (13/40), respectively. When results could be compared, moderate strength of agreement (kappa = .45) was demonstrated. No correlation was found between DNA ploidy by FCM, ICM or combined FCM-ICM and survival time (P = .80, P = .35, and P = .54, respectively)., Conclusion: Approximately 59% of DNA histograms contained aneuploid cell populations. Although ICM, as compared to FCM, is more sensitive in assessing the ploidy status of DBDC, both methods were complementary. Most discrepancies between FCM and ICM were due to the dilution of aneuploid populations by non-neoplastic diploid cells. DNA ploidy assessment in DBDC did not offer the possibility of improving the ability to predict survival.
- Published
- 1999
33. Lung-resistance-related protein expression is a negative predictive factor for response to conventional low but not to intensified dose alkylating chemotherapy in multiple myeloma.
- Author
-
Raaijmakers HG, Izquierdo MA, Lokhorst HM, de Leeuw C, Belien JA, Bloem AC, Dekker AW, Scheper RJ, and Sonneveld P
- Subjects
- Adult, Aged, Aged, 80 and over, Antineoplastic Agents, Alkylating therapeutic use, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Bone Marrow Cells chemistry, Disease-Free Survival, Drug Resistance, Multiple, Drug Resistance, Neoplasm, Female, Humans, Male, Melphalan therapeutic use, Middle Aged, Multiple Myeloma metabolism, Plasma Cells chemistry, Prednisone administration & dosage, Prednisone therapeutic use, Prognosis, Remission Induction, Survival Rate, Treatment Outcome, Antineoplastic Agents, Alkylating administration & dosage, Melphalan administration & dosage, Multiple Myeloma drug therapy, Neoplasm Proteins analysis, Vault Ribonucleoprotein Particles
- Abstract
This study was undertaken to assess the significance of lung-resistance related protein (LRP) expression in plasma cells from untreated multiple myeloma (MM) patients and to determine whether LRP was associated with a poor response and survival in patients treated with different dose regimens of melphalan. Seventy untreated patients received conventional oral dose melphalan (0.25 mg/kg, day 1 to 4) combined with prednisone (MP) or intravenous intermediate-IDM; 70 mg/m2) or high- (140 mg/m2) dose Melphalan (HDM). LRP expression was assessed with immunocytochemistry using the LRP-56 monoclonal antibody. LRP expression was found in 47% of patients. In the MP treated patients, LRP expression was a significant prognostic factor regarding response induction (P < .05), event free survival (P < .003), and overall survival (P < .001). In the intensified dose melphalan treated patients LRP did not have a prognostic value. The response rates of LRP-positive patients to MP and IDM/HDM were 18% versus 81%, respectively (P < .0001). We conclude that LRP is frequently expressed in untreated MM patients and is an independent predictor for response and survival in patients treated with MP. Pretreatment assessment of LRP identifies a subpopulation of patients with a poor probability of response to conventional dose melphalan. Dose intensification of melphalan is likely to overcome LRP-mediated resistance.
- Published
- 1998
34. Three-dimensional confocal laser scanning DNA ploidy cytometry in thick histological sections.
- Author
-
Tekola P, Baak JP, van Ginkel HA, Belien JA, van Diest PJ, Broeckaert MA, and Schuurmans LT
- Subjects
- Animals, Breast Neoplasms genetics, Humans, Image Processing, Computer-Assisted, Liver, Male, Rats, Testis, Image Cytometry methods, Microscopy, Confocal, Ploidies
- Abstract
DNA ploidy measurement by flow (FCM) or image cytometry (ICM) of single cell suspensions of solid tumour has prognostic value, but it would be a definite advantage if the assessment could be done on histological sections. However, this is usually not possible by means of standard ICM, due to the capping of nuclei in thin sections, or overlap in thick sections. Three-dimensional (3D) microscopy by means of confocal laser scanning microscopy (CLSM) could solve this problem in theory but the results published so far are not very satisfactory. A new method has been developed in which the DNA content of haploid (human testis spermatozoa), diploid, tetraploid, octaploid (human and rat liver and human spermatogonia), and near-triploid (human breast cancer) nuclei stained with YOYO-1 iodide has been measured by a newly developed 3D image cytometry method (3DICM) in 20 microns thick histological sections. YOYO-1 iodide is a new highly sensitive, specific, stoichiometric, and stable fluorescent dye for DNA. DNA ploidy of a breast cancer which was near-triploid with FCM and ICM was also assessed with 3DICM in a tissue section adjacent to the section used for FCM and ICM and the results were compared. The integrated 3DICM fluorescence intensity showed good linearity (r = 0.99) with the real DNA content of all nuclei analysed. In human tissue, the coefficient of variation of 3DICM for haploid (n = 12), diploid (n = 63), triploid (n = 13), tetraploid (n = 12), and octaploid (n = 3) ploidy distributions was 5.1, 6.6, 4.2, 4.0, and 0.6 per cent, respectively (n = the number of nuclei). For the rat liver, the CV of the diploid (n = 21), tetraploid (n = 31), and octaploid (n = 3) peaks was 6.7, 4.8, and 1.6 per cent, respectively. Repeated "blind' measurements of nuclei with different DNA indices showed excellent reproducibility between different observers (r = 0.98). It is concluded that the 3DICM method used is accurate, reproducible, and clinically feasible in thick histological sections. This is especially important in small lesions, or if the results of DNA ploidy measurement of single cell suspensions (by FCM) or imprints (by ICM) are inadequate.
- Published
- 1996
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.