document

Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors

Rijlaarsdam, M.A. (author), Tax, D.M.J. (author), Gillis, A.J.M. (author), Dorssers, L.C.J. (author), Koestler, D.C. (author), De Ridder, J. (author), Looijenga, L.H.J. (author)

The cell of origin of the five subtypes (I-V) of germ cell tumors (GCTs) are assumed to be germ cells from different maturation stages. This is (potentially) reflected in their methylation status as fetal maturing primordial germ cells are globally demethylated during migration from the yolk sac to the gonad. Imprinted regions are erased in the...

journal article 2015

document

Predicting Object Size from Hand Kinematics: A Temporal Perspective

Ansuini, C. (author), Cavallo, A. (author), Koul, A. (author), Jacono, M. (author), Yang, Y. (author), Becchio, C. (author)

Research on reach-to-grasp movements generally concentrates on kinematics values that are expression of maxima, in particular the maximum aperture of the hand and the peak of wrist velocity. These parameters provide a snapshot description of movement kinematics at a specific time point during reach, i.e., the maximum within a set of value, but...

journal article 2015

document

Dynamic Growth and Shrinkage Govern the pH Dependence of RecA Filament Stability

Kim, S.H. (author), Park, J. (author), Joo, C. (author), Kim, D. (author), Ha, T. (author)

RecA proteins form a long stable filament on a single-stranded DNA and catalyze strand exchange reaction. The stability of RecA filament changes dramatically with pH, yet its detailed mechanism is not known. Here, using a single molecule assay, we determined the binding and dissociation rates of RecA monomers at the filament ends at various pH....

journal article 2015

document

Quantification of heterogeneity as a biomarker in tumor imaging: A systematic review

Alic, L. (author), Niessen, W.J. (author), Veenland, J.F. (author)

BACKGROUND: Many techniques are proposed for the quantification of tumor heterogeneity as an imaging biomarker for differentiation between tumor types, tumor grading, response monitoring and outcome prediction. However, in clinical practice these methods are barely used. This study evaluates the reported performance of the described methods and...

journal article 2014

document

Interactive local super-resolution reconstruction of whole-body MRI mouse data: A pilot study with applications to bone and kidney metastases

Dzyubachyk, O. (author), Khmelinskii, A. (author), Plenge, E. (author), Kok, P. (author), Snoeks, T.J. (author), Poot, D.H. (author), Löwik, C.W. (author), Botha, C.P. (author), Niessen, W.J. (author), Van der Weerd, L. (author), Meijering, E. (author), Lelieveldt, B.P.F. (author)

In small animal imaging studies, when the locations of the micro-structures of interest are unknown a priori, there is a simultaneous need for full-body coverage and high resolution. In MRI, additional requirements to image contrast and acquisition time will often make it impossible to acquire such images directly. Recently, a resolution...

journal article 2014

document

Skewed brownian fluctuations in single-molecule magnetic tweezers.

Burnham, D.R. (author), De Vlaminck, I. (author), Henighan, T. (author), Dekker, C. (author)

Measurements in magnetic tweezers rely upon precise determination of the position of a magnetic microsphere. Fluctuations in the position due to Brownian motion allows calculation of the applied force, enabling deduction of the force-extension response function for a single DNA molecule that is attached to the microsphere. The standard approach...

journal article 2014

document

Disease Prevention: Saving Lives or Reducing Health Care Costs?

Grootjans-van Kampen, I. (author), Engelfriet, P.M. (author), Van Baal, P.H.M. (author)

Background Disease prevention has been claimed to reduce health care costs. However, preventing lethal diseases increases life expectancy and, thereby, indirectly increases the demand for health care. Previous studies have argued that on balance preventing diseases that reduce longevity increases health care costs while preventing non-fatal...

journal article 2014

document

Blind predictions of DNA and RNA tweezers experiments with force and torque

Chou, F.C. (author), Lipfert, J. (author), Das, R. (author)

Single-molecule tweezers measurements of double-stranded nucleic acids (dsDNA and dsRNA) provide unprecedented opportunities to dissect how these fundamental molecules respond to forces and torques analogous to those applied by topoisomerases, viral capsids, and other biological partners. However, tweezers data are still most commonly...

journal article 2014

document

Lack of Genomic Heterogeneity at High-Resolution aCGH between Primary Breast Cancers and Their Paired Lymph Node Metastases

Vollebergh, M.A. (author), Klijn, C. (author), Schouten, P.C. (author), Wesseling, J. (author), Israeli, D. (author), Ylstra, B. (author), Wessels, L.F.A. (author), Jonkers, J. (author), Linn, S.C. (author)

Lymph-node metastasis (LNM) predict high recurrence rates in breast cancer patients. Systemic treatment aims to eliminate (micro)metastatic cells. However decisions regarding systemic treatment depend largely on clinical and molecular characteristics of primary tumours. It remains, however, unclear to what extent metastases resemble the cognate...

journal article 2014

document

Evaluating Contextual Processing in Diffusion MRI: Application to Optic Radiation Reconstruction for Epilepsy Surgery

Tax, C.M.W. (author), Duits, R. (author), Vilanova, A. (author), Ter Haar Romeny, B.M. (author), Hofman, P. (author), Wagner, L. (author), Leemans, A. (author), Ossenblok, P. (author)

Diffusion MRI and tractography allow for investigation of the architectural configuration of white matter in vivo, offering new avenues for applications like presurgical planning. Despite the promising outlook, there are many pitfalls that complicate its use for (clinical) application. Amongst these are inaccuracies in the geometry of the...

journal article 2014

document

Sandbox University: Estimating Influence of Institutional Action

Forsman, J. (author), Mann, R.P. (author), Linder, A.D. (author), Van den Bogaard, M.E.D. (author)

The approach presented in this article represents a generalizable and adaptable methodology for identifying complex interactions in educational systems and for investigating how manipulation of these systems may affect educational outcomes of interest. Multilayer Minimum Spanning Tree and Monte-Carlo methods are used. A virtual Sandbox...

journal article 2014

document

Balance asymmetry in Parkinson's disease and its contribution to freezing of gait

Boonstra, T.A. (author), Van Vugt, J.P.P. (author), Van der Kooij, H. (author), Bloem, B.R. (author)

Balance control (the ability to maintain an upright posture) is asymmetrically controlled in a proportion of patients with Parkinson’s disease. Gait asymmetries have been linked to the pathophysiology of freezing of gait. We speculate that asymmetries in balance could contribute to freezing by a) hampering the unloading of the stepping leg and...

journal article 2014

document

Development and Validation of Intracranial Thrombus Segmentation on CT Angiography in Patients with Acute Ischemic Stroke

Santos, E.M.M. (author), Marquering, H.A. (author), Berkhemer, O.A. (author), Van Zwam, W.H. (author), Van der Lugt, A. (author), Majoie, C.B. (author), Niessen, W.J. (author)

Background and Purpose: Thrombus characterization is increasingly considered important in predicting treatment success for patients with acute ischemic stroke. The lack of intensity contrast between thrombus and surrounding tissue in CT images makes manual delineation a difficult and time consuming task. Our aim was to develop an automated...

journal article 2014

document

Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities

De Ridder, J. (author), Meysman, P. (author), Oluwagbemi, O. (author), Abeel, T. (author)

Contributing to a student organization, such as the International Society for Computational Biology Student Council (ISCB-SC) and its Regional Student Group (RSG) program, takes time and energy. Both are scarce commodities, especially when you are trying to find your place in the world of computational biology as a graduate student. It comes as...

journal article 2014

document

Gliding Swifts Attain Laminar Flow over Rough Wings

Lentink, D. (author), De Kat, R. (author)

Swifts are among the most aerodynamically refined gliding birds. However, the overlapping vanes and protruding shafts of their primary feathers make swift wings remarkably rough for their size. Wing roughness height is 1–2% of chord length on the upper surface—10,000 times rougher than sailplane wings. Sailplanes depend on extreme wing...

journal article 2014

document

Characterization of the RnfB and RnfG Subunits of the Rnf Complex from the Archaeon Methanosarcina acetivorans

Suharti, S. (author), Wang, M. (author), De Vries, S. (author), Ferry, J.G. (author)

Rnf complexes are redox-driven ion pumps identified in diverse species from the domains Bacteria and Archaea, biochemical characterizations of which are reported for two species from the domain Bacteria. Here, we present characterizations of the redox-active subunits RnfG and RnfB from the Rnf complex of Methanosarcina acetivorans, an acetate...

journal article 2014

document

Quantification of Blood Flow and Topology in Developing Vascular Networks

Kloosterman, A. (author), Hierck, B. (author), Westerweel, J. (author), Poelma, C. (author)

Since fluid dynamics plays a critical role in vascular remodeling, quantification of the hemodynamics is crucial to gain more insight into this complex process. Better understanding of vascular development can improve prediction of the process, and may eventually even be used to influence the vascular structure. In this study, a methodology to...

journal article 2014

document

Mapping Intravascular Ultrasound Controversies in Interventional Cardiology Practice

Maresca, D. (author), Adams, S. (author), Maresca, B. (author), Van der Steen, A.F.W. (author)

Intravascular ultrasound is a catheter-based imaging modality that was developed to investigate the condition of coronary arteries and assess the vulnerability of coronary atherosclerotic plaques in particular. Since its introduction in the clinic 20 years ago, use of intravascular ultrasound innovation has been relatively limited. Intravascular...

journal article 2014

document

A Meta-Analysis on the Relationship between Self-Reported Presence and Anxiety in Virtual Reality Exposure Therapy for Anxiety Disorders

Ling, Y. (author), Nefs, H.T. (author), Nexhmedin, M. (author), Heynderickx, I. (author), Brinkman, W.P. (author)

In virtual reality exposure therapy (VRET) for anxiety disorders, sense of presence in the virtual environment is considered the principal mechanism that enables anxiety to be felt. Existing studies on the relation between sense of presence and level of anxiety, however, have yielded mixed results on the correlation between the two. In this meta...

journal article 2014

document

Atherosclerotic Plaque Component Segmentation in Combined Carotid MRI and CTA Data Incorporating Class Label Uncertainty

Van Engelen, A. (author), Niessen, W.J. (author), Klein, S. (author), Groen, H.C. (author), Verhagen, H.J.M. (author), Wentzel, J.J. (author), Van der Lugt, A. (author), De Bruijne, M. (author)

Atherosclerotic plaque composition can indicate plaque vulnerability. We segment atherosclerotic plaque components from the carotid artery on a combination of in vivo MRI and CT-angiography (CTA) data using supervised voxelwise classification. In contrast to previous studies the ground truth for training is directly obtained from 3D registration...

journal article 2014