Arthemis: annotation software in an integrated capturing and analysis system for colonoscopy

Colonoscopy is an endoscopic technique that allows physicians to inspect the inside of the human colon. During a colonoscopic procedure, a tiny video camera at the tip of the endoscope generates a video signal of the internal mucosa of the colon. In current practice, the entire colonoscopic procedure is not routinely captured. Software tools providing easy access to important contents of videos that are digitally captured during colonoscopy are not available. Hence, it is very time consuming to review an entire video, locate important contents, annotate them, and extract the annotated contents for research, teaching, and training purposes. Arthemis, a software application, was developed to facilitate this process. For convenient data sharing, Arthemis allows annotation according to the European Gastrointestinal Society for Endoscopy (ESGE) Minimal Standard Terminology (MST), an internationally accepted standard for digestive endoscopy. Arthemis is part of our integrated capturing and content analysis system for colonoscopy called Endoscopic Multimedia Information System (EMIS). This paper presents Arthemis as a component of EMIS, the design and implementation of Arthemis, and key lessons learned from the development process.     

A neural network for predicting the stability of RNA/DNA hybrid duplexes

A back propagation (BP) neural network (NN) method has been developed to predict the stability of RNA/DNA duplex. Calculated T_m of hybrid formation with the present parameters fits the experimental values within reasonable errors (AD=1.2887 K, SEP=1.782, R²=0.9673 for NN1; AD=2.1388 K, SEP=3.506, R²=0.8889 for NN2). And it has the advantage that the determinations of thermodynamic parameters (TP) are not needed.     

Network virtualization as an integrated solution for emergency communication

In this paper the Virtual Private Ad Hoc Networking (VPAN) platform is introduced as an integrated networking solution for many applications that require secure transparent continuous connectivity using heterogeneous devices and network technologies. This is done by creating a virtual logical self-organizing network on top of existing network technologies reducing complexity and maintaining session continuity right from the start. One of the most interesting applications relies in the field of emergency communication with its specific needs which will be discussed in this paper and matched in detail against the architecture and features of the VPAN platform. The concept and dynamics are demonstrated and evaluated with measurements done on real hardware.     

Crisis response strategies in Finland and Spain

Crises are common in today's unpredictable environment rising the importance of crisis response strategies. Two societies in Europe are chosen: Finland, where trust in society is generalized to institutions, and Spain, where trust in society remains on the level of individuals. Using the results of the European Communication Monitor 2013 survey on crisis communication, we explored three hypotheses: “certain types of crises are often met with certain types of strategies,” “cultural context makes some crises more likely than others,” and “cultural context makes some response strategies more likely than others.” We find evidence for all three hypotheses and discuss our findings about perceived differences in the two societies. The results show that the cultural context plays an important role for crisis communication.     

SAPPHIRE: A toolkit for building efficient stream programs for medical video analysis

This paper describes the design and implementation of SAPPHIRE – a novel middleware and software development kit for stream programing on a heterogeneous system of multi-core multi-CPUs with optional hardware accelerators such as graphics processing unit (GPU). A stream program consists of a set of tasks where the same tasks are repeated over multiple iterations of data (e.g., video frames). Examples of such programs are video analysis applications for computer-aided diagnosis and computer-assisted surgeries. Our design goal is to reduce the implementation efforts and ease collaborative software development of stream programs while supporting efficient execution of the programs on the target hardware. To validate the toolkit, we implemented EM-Automated-RT software with the toolkit and reported our experience. EM-Automated-RT performs real-time video analysis for quality of a colonoscopy procedure and provides visual feedback to assist the endoscopist to achieve optimal inspection of the colon during the procedure. The software has been deployed in a hospital setting to conduct a clinical trial.     

Pseudo‐3D RSSI‐based WSN localization algorithm using linear regression

Receiver Strength Signal Indication based Wireless Sensor Networks offer a cheap solution for location‐aware applications. For a final breakthrough these systems need fast deployment and easy auto‐configuration. In this study, we use the real‐life iMinds test bed to expand a two‐dimensional localization algorithm to the pseudo third dimension with very low additional computational time. Our experiments show that this fast three‐dimensional algorithm has no outliers and avoids manual calibration. Our algorithm has lower position errors than a maximum likelihood algorithm with a mean square error cost function. Furthermore, with non‐parametric statistical tests, we show that our previously designed two‐dimensional preprocessing performs equally well in pseudo‐three dimensions: the preprocessing reduces the position error in a statistically significant way.Copyright © 2013 John Wiley & Sons, Ltd.     

Application of bacteria involved in the biological sulfur cycle for paper mill effluent purification

In anaerobic wastewater treatment, the occurrence of biological sulfate reduction results in the formation of unwanted hydrogen sulfide, which is odorous, corrosive and toxic. In this paper, the role and application of bacteria in anaerobic and aerobic sulfur transformations are described and exemplified for the treatment of a paper mill wastewater. The sulfate containing wastewater first passes an anaerobic UASB reactor for bulk COD removal which is accompanied by the formation of biogas and hydrogen sulfide. In an aeration pond, the residual COD_organic and the formed dissolved hydrogen sulfide are removed. The biogas, consisting of CH₄ (80-90 vol.%), CO₂ (10-20 vol.%) and H₂S (0.8-1.2 vol.%), is desulfurised prior to its combustion in a power generator thereby using a new biological process for H₂S removal. This process will be described in more detail in this paper. Biomass from the anaerobic bioreactor has a compact granular structure and contains a diverse microbial community. Therefore, other anaerobic bioreactors throughout the world are inoculated with biomass from this UASB reactor. The sludge was also successfully used in investigation on sulfate reduction with carbon monoxide as the electron donor and the conversion of methanethiol. This shows the biotechnological potential of this complex reactor biomass.     

Substituent distribution within cross-linked and hydroxypropylated sweet potato starch and potato starch

Revealing the substituents distribution within starch can help to understand the changes of starch properties after modification. The distribution of substituents over cross-linked and hydroxypropylated sweet potato starch was investigated and compared with modified potato starch. The starches were cross-linked with sodium trimetaphosphate and/or hydroxypropylated with propylene oxide. The native and modified starches were gelatinized and hydrolysed by pullulanase, β-amylase, α-amylase and a combination of pullulanase, α-amylase and amyloglucosidase. The hydrolysates were analysed by HPSEC, HPAEC and MALDI-TOF mass spectrometry. Cross-linking had only a slight effect on the enzymatic hydrolysis, where hydroxypropylation evidently limited the enzymatic hydrolysis. The results obtained suggest that the hydroxypropyl substituents are not distributed regularly over the starch chains. Although the average substitution was around 2 hydroxypropyl groups per 10 glucose units, in the enzyme digests of hydroxypropylated starches, oligomer fragments of 10–15 glucose units, carrying 5–8 hydroxypropyl groups, were identified. It is hypothesised that higher levels of substituents are present in the amorphous regions and periphery of clusters of starch granules. This is the first time that the location of hydroxypropyl groups within sweet potato starch has been examined in this detail. Despite significant differences in granule architecture between starches from potato and sweet potato, similar patterns of hydroxypropylation have been found.