Realizing the Costs: Template-Based Surface Realisation in the GRAPH Approach to Referring Expression Generation

We describe a new realiser developed for the TUNA 2009 Challenge, and present its evaluation scores on the development set, showing a clear increase in performance compared to last year’s simple realiser

Quantification of calcium signatures in roots of Arabidopsis thaliana

Calcium (Ca2+) is an essential second messenger in plant cells linking the perception of stresses at the plasma membrane to the appropriate defense response. The calcium signature theory states that for each perceived stress there is a unique calcium transient that triggers specific downstream responses. It is thought that the signaling specificity is encoded in the spatio-temporal pattern of cytosolic calcium concentration, which is in turn decoded by various intracellular calcium binding proteins. For 25 years now the calcium signature theory has not been conclusively proven, and alternative theories are now appearing. One of the problems remaining is that there is no standard method to quantify these spatio- temporal signals. The aim of this thesis was to develop a standard method to quantify calcium signatures in plants and start constructing a library of calcium signatures in response to different stresses. As a model system I used Arabidopsis thaliana roots expressing the R-GECO calcium sensor. To quantify the spatio-temporal calcium response, the calcium signature was divided into six quantifiable parameters: (a) delay of the first detected calcium signal, (b) location of the first calcium signal, (c) duration of the calcium signal, (d) distance that the calcium wave traveled along the root, (e) velocity with which the calcium wave travels towards the root tip, and (f) velocity with which the calcium wave travels towards the shoot. Principle component analysis (PCA) was used to look for similarities and analyze the data. Responses to eleven elicitors (ATP, chitin, cellobiose, cold, D-serine, elf18, flg22, glutamate, NaCl, nlp20 and PG3) were tested. The results showed that, indeed, each elicitor resulted in a unique composition of the six parameters that together form the calcium signature. Moreover, calcium signatures in response to biotic versus abiotic elicitors formed two distinct groups. While biotic stress caused delayed calcium responses specific to the elongation zone of plant roots, abiotic stresses resulted in immediate and systemic calcium signatures. Further experiments suggested that ROS play a key role in restricting calcium signatures to the elongation zone in response to biotic stress and in propagation of calcium signals through the root in response to abiotic stress, indicating that there is crosstalk between reactive oxygen species (ROS) and calcium signatures to prioritize distinct stresses

Relevance of ASR for the Automatic Generation of Keywords Suggestions for TV programs

Semantic access to multimedia content in audiovisual archives is to a large extent dependent on quantity and quality of the metadata, and particularly the content descriptions that are attached to the individual items. However, given the growing amount of materials that are being created on a daily basis and the digitization of existing analogue collections, the traditional manual annotation of collections puts heavy demands on resources, especially for large audiovisual archives. One way to address this challenge, is to introduce (semi) automatic annotation techniques for generating and/or enhancing metadata. The NWO funded CATCH-CHOICE project has investigated the extraction of keywords form textual resources related to the TV programs to be archived (context documents), in collaboration with the Dutch audiovisual archives, Sound and Vision. Besides the descriptions of the programs published by the broadcasters on their Websites, Automatic Speech Transcription (ASR) techniques from the CATCH-CHoral project, also provide textual resources that might be relevant for suggesting keywords. This paper investigates the suitability of ASR for generating such keywords, which we evaluate against manual annotations of the documents and against keywords automatically generated from context documents

Insertional Oncogenesis after Retroviral Gene Transfer in Hematopoietic Stem Cells

__Abstract__ This thesis is focuses on the insertional oncogenesis brought about by gamma-retroviral vector insertions. In hematopoietic gene therapy, gamma-retroviral vectors can be used to deliver therapeutic transgenes into target cells of patients with monogenic disorders, which has been successfully shown in three human diseases. The addition of the therapeutic gene to the host cell genome has the opportunity to cure the disorder. The mechanism that allows insertion of the transgene in the host cell genome can unfortunately also introduce deregulation of the genes surrounding the insertion site, sometimes with leukemia as a result. In the studies described here, the insertion profiles in mouse or human hematopoietic cells were analyzed and the frequency of oncogenic mutations was determined. In addition, software that allows automated determination and annotation of retroviral insertion sites was developed

The realization of an integrated Mach-Zehnder waveguide immunosensor in silicon technology

We describe the realization of a symmetric integrated channel waveguide Mach-Zehnder sensor which uses the evanescent field to detect small refractive-index changes (¿nmin ¿ 1 × 10¿4) near the guiding-layer surface. This guiding layer consists of ridge structures with a height of 3 nm and a width of 4 ¿m made in Si3N4. This layer has a thickness of 100 nm. The sensor device has been tested with glucose solutions of different bulk refractive indices. Results of a slab-model calculation are in good agreement with obtained experimental results. The feasibility of applying this sensor for immunosensing, detecting directly the binding of antigen to an antibody receptor surface, is shown with antibody-antigen binding experiments

Can Angiotensin-Converting Enzyme Inhibitors Slow the Progression of Cognitive Decline In Elderly Patients With Dementia?

Background: Dementia is a slow progressing neurodegenerative disease characterized by loss of executive functioning, communication ability, and activities of daily living. With few treatment options currently approved for dementia, angiotensin-converting enzyme inhibitors (ACE-I) have been implicated as a new potential treatment to slow cognitive decline. ACE-I use in dementia, however, is controversial due to conflicting research and new discoveries into the pathophysiology of the brain and ACE. This systematic review aims to evaluate the current research on ACE-I use in cognitive decline. Methods: Exhaustive search of available medical literature databases including Medline (Ovid/PubMed), Google Scholar, Clinical Key, and Web of Science was conducted. Keywords used in the search included: Alzheimer’s disease, dementia, ACE inhibitors, angiotensin converting enzyme inhibitors, cognitive decline, renin-angiotensin system, and RAS. Alzheimer’s disease (AD) and vascular dementia (VaD) was the focus of this review based on the proposed pathophysiology. Studies were included if cognitive assessment tools such as the mini mental status exam, mini-cog or Qmci, were assessed at baseline and an end-point with a minimum of 6 months. Articles were assessed for quality using the GRADE criteria. Results: Five studies met inclusion criteria and were evaluated. Three of the studies found were observational, one study was a randomized controlled trial, and one was a cohort study. With the exception of one very low quality study, the results were consistent that ACE-I may provide slowing of the progression of cognitive decline in dementia patients. Conclusion: Current research on dementia progression and ACE inhibitors, as measured by cognitive assessment tools, have been shown to slow cognitive decline in elderly patients. Further research, preferably multiple, large randomized controlled human trials are necessary to determine the risk versus benefit of ACE inhibitor use. Keywords: Alzheimer’s disease, dementia, ACE inhibitors, angiotensin converting enzyme inhibitors, cognitive decline, renin-angiotensin system, RAS

In the Truman show: generating dynamic scenarios in a driving simulator

All the devices, animals, and people make their decisions based on what you're doing, but you don't know it or even notice it. Your world is that of Truman Burbank, from the 1998 movie The Truman Show. With this idea in mind, we've taken the movie metaphor to implement a prototype simulation system where the user steps into Truman's shoes. The set of our "movie" is a driving simulator, and the user is learning to drive a car. During the driving lessons, users drive in a virtual world that lets them experience all kinds of traffic scenarios. The system generates the scenarios with the student as the focal point, and the other traffic entities respond to the student's behavior, without the student noticing. To control the traffic scenarios and make them more effective, our prototype employs an agent-based framework. In this framework, each entity in the simulator is an actor agent playing a role. The prototype also includes a hierarchy of directors that directs the main action and the behind-the-scenes activity. The advantage of the movie metaphor is that it helps separate scenario description from scenario playing. The agents can read their required information from a script and perform their actions based on that information. Using this framework lets us build software that's extensible, maintainable, and easy to understan