Hyperspectral Data Analysis in R: The hsdar Package

Hyperspectral remote sensing is a promising tool for a variety of applications including ecology, geology, analytical chemistry and medical research. This article presents the new hsdar package for R statistical software, which performs a variety of analysis steps taken during a typical hyperspectral remote sensing approach. The package introduces a new class for efficiently storing large hyperspectral data sets such as hyperspectral cubes within R. The package includes several important hyperspectral analysis tools such as continuum removal, normalized ratio indices and integrates two widely used radiation transfer models. In addition, the package provides methods to directly use the functionality of the caret package for machine learning tasks. Two case studies demonstrate the package's range of functionality: First, plant leaf chlorophyll content is estimated and second, cancer in the human larynx is detected from hyperspectral data

Indomethacin induces apoptosis via a MRP1-dependent mechanism in doxorubicin-resistant small-cell lung cancer cells overexpressing MRP1

Small-cell lung cancers (SCLCs) initially respond to chemotherapy, but are often resistant at recurrence. The non-steroidal anti-inflammatory drug indomethacin is an inhibitor of multidrug resistance protein 1 (MRP1) function. The doxorubicin-resistant MRP1-overexpressing human SCLC cell line GLC4-Adr was highly sensitive for indomethacin compared with the parental doxorubicin-sensitive line GLC4. The purpose of this study was to analyse the relationship between hypersensitivity to indomethacin and MRP1 overexpression. The experimental design involved analysis of the effect of MRP1 downregulation on indomethacin-induced cell survival and apoptosis in GLC4-Adr and GLC4, using siRNA. In addition the effect of indomethacin on glutathione levels and mitochondrial membrane potential was investigated. Small interfering RNAs directed against MRP1 reduced MRP1 mRNA levels twofold and reduced efflux pump function of MRP1, which was reflected by a 1.8-fold higher accumulation of MRP1 substrate carboxyfluorescein, in si-MRP1 versus si-Luciferase-transfected GLC4-Adr cells. Multidrug resistance protein 1 downregulation decreased initial high apoptosis levels 2-fold in GLC4-Adr after indomethacin treatment for 24 h, and increased cell survival (IC50) from 22.8±2.6 to 30.4±5.1 μM following continuous indomethacin exposure. Multidrug resistance protein 1 downregulation had no effect on apoptosis in GLC4 or on glutathione levels in both lines. Although indomethacin (20 μM) for 2 h decreased glutathione levels by 31.5% in GLC4-Adr, complete depletion of cellular glutathione by L-buthionine (S,R)-sulphoximine only resulted in a small increase in indomethacin-induced apoptosis in GLC4-Adr, demonstrating that a reduced cellular glutathione level is not the primary cause of indomethacin-induced apoptosis. Indomethacin exposure decreased mitochondrial membrane potential in GLC4-Adr cells, suggesting activation of the mitochondrial apoptosis pathway. Indomethacin induces apoptosis in a doxorubicin-resistant SCLC cell line through an MRP1-dependent mechanism. This may have implications for the treatment of patients with MRP1-overexpressing tumours

Vandaag heb ik mijn woorden bij de hand; communicatieve vaardigheden en sociale participatie bij mensen met afasie in de revalidatiefase

In dit onderzoek is de relatie tussen de verbale en non-verbale communicatieve vaardigheden van afasiepatiënten en de mate van sociale participatie in de maatschappij onderzocht. Bij acht mensen met een afasie lichte tot ernstige afasie zijn op twee momenten drie testen afgenomen: de Nederlandse Community Integration Questionnaire-Afasie, de Analyse Spontane Taal bij Afasiepatiënten en de Scenario Test. In de tussentijd kregen de participanten logopedische therapie. Uit dit onderzoek blijkt dat er na een periode van logopedische behandeling een vooruitgang zichtbaar is in de verbale communicatie. Deze vooruitgang is echter niet gerelateerd aan de mate van sociale participatie. De mate van sociale participatie in de gemeenschap is op beide momenten laag.

How To Determine the Phreatic Surface in a Dike during Storm Conditions with Wave Overtopping: A Method Applied to the Afsluitdijk

The most famous dam of the Netherlands, the Afsluitdijk, is in need of renovation. Hydraulic conditions for the year 2050, for some aspects even 2100, must be considered during the renovation of the dam originally constructed 1927-1933. A combination of sea level rise due to climate change and a change in the applied statistical methods result in design conditions that are, at some locations, meters higher than those used a century ago. In a mission to retain the required level of safety while keeping expenses at a minimum, several innovative designs are considered; one of which is to allow very large overtopping discharges by making the dam resilient to erosion. However, calculations have shown that the overtopping values can be over 10 litres per second per meter dam, and the effect of this overtopping on the Afsluitdijk is unknown. In Dutch national design guidelines for dikes, schematizations are proposed for the phreatic surface in dikes during storm conditions. Wave overtopping is mentioned to have a rising effect on the phreatic surface, but clear methods to determine the magnitude of this effect are not prescribed. The guidelines suggest assuming full saturation of the dam in severe overtopping conditions, which has a detrimental effect on the slope stability. Recent studies and large scale infiltration tests on the Afsluitdijk show that only a very limited amount of water infiltrates in the dam and that the assumption of full saturation is much too conservative in case of the Afsluitdijk. In the present study, a finite-element model (Plaxflow) is used to model the phreatic surface in the Afsluitdijk during storm conditions, taking into account the effect of wave overtopping on the phreatic line. Parameters were determined by in-situ and laboratory investigations. To verify the model, calculations were calibrated on standpipe measurements. Wave overtopping is modelled by defining infiltration boundaries based on experiments and sensitivity analyses are conducted. The result of the study is a phreatic surface that can safely be used for the calculation of the slope stability of the levee during predicted storm conditions for the year 2050

Ink bleed-through removal of historical manuscripts based on hyperspectral imaging

Old manuscripts can be degraded by different reasons over time. The ink bleed-through from the back side of the page is a common problem which compromises the readability and the aesthetics of the document. Unsupervised bleed-through removal is a challenging task as pixel intensity of bleed-through areas can be very similar to fine-details of the writing. This paper provides a brief review about state-of-the-art methods for bleed-through removal. Moreover, we propose an algorithm for the segmentation of the bleed-through areas from a manuscript collected from the National Library of Oslo using hyperspectral imaging. This work also presents the restoration of the collected manuscript applying inpainting algorithms based on our segmentation approach

Hyperspectral Imaging Using Flexible Endoscopy for Laryngeal Cancer Detection

Hyperspectral imaging (HSI) is increasingly gaining acceptance in the medical field. Up until now, HSI has been used in conjunction with rigid endoscopy to detect cancer in vivo. The logical next step is to pair HSI with flexible endoscopy, since it improves access to hard-to-reach areas. While the flexible endoscope’s fiber optic cables provide the advantage of flexibility, they also introduce an interfering honeycomb-like pattern onto images. Due to the substantial impact this pattern has on locating cancerous tissue, it must be removed before the HS data can be further processed. Thereby, the loss of information is to minimize avoiding the suppression of small-area variations of pixel values. We have developed a system that uses flexible endoscopy to record HS cubes of the larynx and designed a special filtering technique to remove the honeycomb-like pattern with minimal loss of information. We have confirmed its feasibility by comparing it to conventional filtering techniques using an objective metric and by applying unsupervised and supervised classifications to raw and pre-processed HS cubes. Compared to conventional techniques, our method successfully removes the honeycomb-like pattern and considerably improves classification performance, while preserving image details