document

Reliability of System Identification Techniques to Assess Standing Balance in Healthy Elderly

Pasma, J.H. (author), Engelhart, D. (author), Maier, A.B. (author), Aarts, R.G.K.M. (author), Van Gerven, J.M.A. (author), Arendzen, J.H. (author), Schouten, A.C. (author), Meskers, C.G.M. (author), Van der Kooij, H. (author)

Objectives System identification techniques have the potential to assess the contribution of the underlying systems involved in standing balance by applying well-known disturbances. We investigated the reliability of standing balance parameters obtained with multivariate closed loop system identification techniques. Methods In twelve healthy...

journal article 2016

document

2D Representation of Transcriptomes by t-SNE Exposes Relatedness between Human Tissues

Taskesen, E. (author), Reinders, M.J.T. (author)

The GTEx Consortium reported that hierarchical clustering of RNA profiles from 25 unique tissue types among 1641 individuals accurately distinguished the tissue types, but a multidimensional scaling failed to generate a 2D projection of the data that separates tissue-subtypes. In this study we show that a projection by t-Distributed Stochastic...

journal article 2016

document

Automated entire thrombus density measurements for robust and comprehensive thrombus characterization in patients with acute ischemic stroke

Santos, E.M.M. (author), Niessen, W.J. (author), Yoo, A.J. (author), Berkhemer, O.A. (author), Beenen, L.F. (author), Majoie, C.B. (author), Marquering, H.A. (author)

journal article 2016

document

Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction

Winglee, K. (author), McGuire, A.M. (author), Maiga, M. (author), Abeel, T.E.P.M.F. (author), Shea, T. (author), Desjardins, C.A. (author), Diarra, B. (author), Baya, B. (author), Sanogo, M. (author), Diallo, S. (author), Earl, A. (author), Bishai, W.R. (author)

Background Mycobacterium africanum, made up of lineages 5 and 6 within the Mycobacterium tuberculosis complex (MTC), causes up to half of all tuberculosis cases in West Africa, but is rarely found outside of this region. The reasons for this geographical restriction remain unknown. Possible reasons include a geographically restricted animal...

journal article 2016

document

Olfactomedin 4 serves as a marker for disease severity in pediatric respiratory syncytial virus (RSV) infection

Brand, H.K. (author), Ahout, I.M.L. (author), De Ridder, D. (author), Diepen, A. (author), Li, Y. (author), Zaalberg, M. (author), Andeweg, A. (author), Roeleveld, N. (author), De Groot, R. (author), Warris, A. (author), Hermans, P.W.M. (author), Ferwerda, G. (author), Staal, F.J.T. (author)

Background Respiratory viral infections follow an unpredictable clinical course in young children ranging from a common cold to respiratory failure. The transition from mild to severe disease occurs rapidly and is difficult to predict. The pathophysiology underlying disease severity has remained elusive. There is an urgent need to better...

journal article 2015

document

Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting

Vlijm, R. (author), Torre, J. (author), Dekker, C. (author)

The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a...

journal article 2015

document

Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes

Vlijm, R. (author), Lee, M. (author), Ordu, O. (author), Boltengagen, A. (author), Lusser, A. (author), Dekker, N.H. (author), Dekker, C. (author)

Eukaryotic nucleosomes consists of an (H3-H4)2 tetramer and two H2A-H2B dimers, around which 147 bp of DNA are wrapped in 1.7 left-handed helical turns. During chromatin assembly, the (H3-H4)2 tetramer binds first, forming a tetrasome that likely constitutes an important intermediate during ongoing transcription. We recently showed that (H3-H4)2...

journal article 2015

document

Improving the pH-stability of Versatile Peroxidase by Comparative Structural Analysis with a Naturally-Stable Manganese Peroxidase (+ correction)

Saez-Jimenez, V. (author), Fernandez Fueyo, E. (author), Madrano, F.J. (author), Romero, A. (author), Martinez, A.T. (author), Ruiz-Duenas, F.J. (author)

Versatile peroxidase (VP) from the white-rot fungus Pleurotus eryngii is a high redox potential peroxidase of biotechnological interest able to oxidize a wide range of recalcitrant substrates including lignin, phenolic and non-phenolic aromatic compounds and dyes. However, the relatively low stability towards pH of this and other fungal...

journal article 2015

document

Correction: Quantitative Localization Microscopy: Effects of Photophysics and Labeling Stoichiometry

Nieuwenhuizen, R.P.J. (author), Bates, M. (author), Szymborska, A. (author), Lidke, K.A. (author), Rieger, B. (author), Stallinga, S. (author)

journal article 2015

document

Integrated Analysis and Visualization of Group Differences in Structural and Functional Brain Connectivity: Applications in Typical Ageing and Schizophrenia

Langen, C.D. (author), White, T. (author), Ikram, M.A. (author), Vernooij, M.W. (author), Niessen, W.J. (author)

Structural and functional brain connectivity are increasingly used to identify and analyze group differences in studies of brain disease. This study presents methods to analyze uni- and bi-modal brain connectivity and evaluate their ability to identify differences. Novel visualizations of significantly different connections comparing multiple...

journal article 2015

document

Lighting to make you feel better: Improving the mood of elderly people with affective ambiences

Kuijsters, A. (author), Redi, J.A. (author), De Ruyter, B. (author), Heynderickx, I.E.J.R. (author)

Current lighting technologies extend the options for changing the appearance of rooms and closed spaces, as such creating ambiences with an affective meaning. Using intelligence, these ambiences may instantly be adapted to the needs of the room’s occupant(s), possibly improving their well-being. We hypothesized that ambiences with a clearly...

journal article 2015

document

Co-Orientation: Quantifying Simultaneous Co-Localization and Orientational Alignment of Filaments in Light Microscopy

Nieuwenhuizen, R.P.J. (author), Nahidiazar, L. (author), Manders, E.M.M. (author), Jalink, K. (author), Stallinga, S. (author), Rieger, B. (author)

Co-localization analysis is a widely used tool to seek evidence for functional interactions between molecules in different color channels in microscopic images. Here we extend the basic co-localization analysis by including the orientations of the structures on which the molecules reside. We refer to the combination of co-localization of...

journal article 2015

document

Co-Orientation: Quantifying Simultaneous Co-Localization and Orientational Alignment of Filaments in Light Microscopy

Nieuwenhuizen, R.P.J. (author), Nahidiazar, L. (author), Manders, E.M.M. (author), Jalink, K. (author), Stallinga, S. (author), Rieger, B. (author)

Co-localization analysis is a widely used tool to seek evidence for functional interactions between molecules in different color channels in microscopic images. Here we extend the basic co-localization analysis by including the orientations of the structures on which the molecules reside. We refer to the combination of co-localization of...

journal article 2015

document

Quantitative Localization Microscopy: Effects of Photophysics and Labeling Stoichiometry

Nieuwenhuizen, R.P.J. (author), Bates, M. (author), Szymborska, A. (author), Lidke, K.A. (author), Rieger, B. (author), Stallinga, S. (author)

Quantification in localization microscopy with reversibly switchable fluorophores is severely hampered by the unknown number of switching cycles a fluorophore undergoes and the unknown stoichiometry of fluorophores on a marker such as an antibody. We overcome this problem by measuring the average number of localizations per fluorophore, or...

journal article 2015

document

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

Gritsenko, A.A. (author), Hulsman, M. (author), Reinders, M.J.T. (author), De Ridder, D. (author)

Translation of RNA to protein is a core process for any living organism. While for some steps of this process the effect on protein production is understood, a holistic understanding of translation still remains elusive. In silico modelling is a promising approach for elucidating the process of protein synthesis. Although a number of...

journal article 2015

document

Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex

Babaei, S. (author), Mahfouz, A.M.E.T.A. (author), Hulsman, M. (author), Lelieveldt, B.P.F. (author), De Ridder, J. (author), Reinders, M.J.T. (author)

The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains...

journal article 2015

document

Morphologic and Aerodynamic Considerations Regarding the Plumed Seeds of Tragopogon pratensis and Their Implications for Seed Dispersal

Casseau, V. (author), De Croon, G.C.H.E. (author), Izzo, D. (author), Pandolfi, C. (author)

Tragopogon pratensis is a small herbaceous plant that uses wind as the dispersal vector for its seeds. The seeds are attached to parachutes that increase the aerodynamic drag force and increase the total distance travelled. Our hypothesis is that evolution has carefully tuned the air permeability of the seeds to operate in the most convenient...

journal article 2015

document

Short-Range Guiding Can Result in the Formation of Circular Aggregates in Myxobacteria Populations

Janulevicius, A. (author), Van Loosdrecht, M.C.M. (author), Picioreanu, C. (author)

Myxobacteria are social bacteria that upon starvation form multicellular fruiting bodies whose shape in different species can range from simple mounds to elaborate tree-like structures. The formation of fruiting bodies is a result of collective cell movement on a solid surface. In the course of development, groups of flexible rod-shaped cells...

journal article 2015

document

Hands-Free Image Capture, Data Tagging and Transfer Using Google Glass: A Pilot Study for Improved Wound Care Management

Aldaz, G. (author), Shluzas, L.A. (author), Pickham, D. (author), Eris, O. (author), Sadler, J. (author), Joshi, S. (author), Leifer, L. (author)

Chronic wounds, including pressure ulcers, compromise the health of 6.5 million Americans and pose an annual estimated burden of $25 billion to the U.S. health care system. When treating chronic wounds, clinicians must use meticulous documentation to determine wound severity and to monitor healing progress over time. Yet, current wound...

journal article 2015

document

Biochemical, Transcriptomic and Proteomic Analyses of Digestion in the Scorpion Tityus serrulatus: Insights into Function and Evolution of Digestion in an Ancient Arthropod

Fuzita, F.J. (author), Pinkse, M.W.H. (author), Patane, J.S.L. (author), Juliano, M.A. (author), Verhaert, P.D.E.M. (author), Lopes, A.R. (author)

Scorpions are among the oldest terrestrial arthropods and they have passed through small morphological changes during their evolutionary history on land. They are efficient predators capable of capturing and consuming large preys and due to envenomation these animals can become a human health challenge. Understanding the physiology of scorpions...

journal article 2015