Spores in dairy – new insights in detection,enumeration and risk assessment

The performance of the ISO method for the ‘Enumeration of the Specially Thermoresistant Spores of Thermophilic Bacteria in Dried Milk’ (ISO/TS27265; 2009) was compared with a more practical method. Both were tested for predictability of spoilage of UHT treated reconstituted milk. The data show that heating for 30 min at 100 °C has the same predictive value as heating for 30 min at 106 °C, provided that specifications are increased 1 log₁₀ and the use of TSA as a cultivation medium is recommended over PCMA. Predictability of spoilage using classical plating methods is furthermore discussed in relation to variation in spore heat resistance of spores commonly present in the dairy industry.     

Delineating the Model-Stakeholder Gap: Framing Perceptions to Analyse the Information Requirement in River Management

Computer models can support policy development in environmental management, but often suffer from a lack of practical application. This is part due to a ‘gap’ between the ways in which various participants in the policy process deal with information. The framework described in this paper provides a structured approach to information analysis in policy processes. The awareness of differences in the nature of information helps in dealing with different perceptions and actor backgrounds during this policy process because it allows a better match between the information needs and the tools or procedures that are applied. Construal level theory, originating from consumer psychology, can account for some differences that remained unaddressed so far and forms a key component of this framework. Application of the framework to the Dutch Maas case shows that a gap between the model and its users is unavoidable; model applications are dominated by the fairly technical conceptions which modelers have of the system, and fail to address high level construals brought up by the stakeholders. Application of the framework can support the match between mutual expectations of modelers and users.     

The position of the structurally autonomous kringle 2 domain influences the functional features of tissue-type plasminogen activator

Tissue-type plasminogen activator (t-PA) is composed of structurallyautonomous domains. From the N-terminus of t-PA, a finger-likedomain (F), an epidermal growth factor-like domain (G), twokringle domains (Kl and K2) and a serine protease domain (P)can be discerned. The K2 domain of t-PA is known to be involvedin lysine binding, fibrin binding and fibrin-dependent plasminogenactivation. To study the functional autonomy of the K2 domainin t-PA we constructed, with the aid of a cassette t-PA gene[Rehberg et al. (1989) Protein Engng, 2,371–377], mutantt-PA genes coding for four molecules (FGK1K2P, FGK2K1P, GK1K2Pand GK2K1P) in which the K2 domain was placed in two differentpositions in t-PA. The DNAs of wild-type t-PA and the t-PA variantswere expressed in Chinese hamster ovary cells and the recombinantproteins were purified by affinity chromatography.All moleculeswere expressed in their single-chain form and could be convertedto their two-chain form. With these molecules, lysine binding,fibrin binding and fibrin-dependent plasminogen activation werestudied. All variants showed affinity for lysyl-Sepharose andaminohexyl-Sepharose. Reversal of the K domains (FGK2K1P versusFGK2K1P and GK1K2P versus GK2K1P) resulted in a 23–47%weaker interaction to both lysyl-Sepharose and aminohexyl-Sepharose.Deleting the F domain (FGK1K2P versus GK1K2P and FGK2K1P versusGK2K1P) resulted in a 20–70% improvement of the interactionslysyl-Sepharose and aminohexyl-Sepharose. All variants boundto a forming fibrin clot. Reversal of the K domains (FGK1K2Pversus FGK2K1P) reduced fibrin binding. In the presence of thelysine analogue -amino caproic acid, only FGK1K2P bound to fibrin.All variants activated plasminogen. In the absence of fibrinogenCNBr fragments (mimic of fibrin), the reversal of the K domain(FGK2K1P) resulted in a 2-fold improved plasminogen activation.In the presence of a fibrin mimic, the plasminogen activationsof the F domain deletion analogues GK1K2P and GK2K1P were foundto be decreased 2- to 4-fold. From these results we concludedthat the function of t-PA in lysine binding, fibrin bindingand fibrin-dependent plasminogen activation is dependent onthe correct spatial orientation of the K2 domain within thet-PA molecule     

Information access in multimedia databases based on feature models

With the increasing popularity of the WWW, the main challenge in computer science has become content-based retrieval of multimedia objects. Access to multimedia objects in databases has long been limited to the information provided in manually assigned keywords. Now, with the integration of feature-detection algorithms in database systems software, content-based retrieval can be fully integrated with query processing. We describe our experimentation platform under development, making database technology available to multimedia. Our approach is based on the new notion of feature databases. Its architecture fully integrates traditional query processing and content-based retrieval techniques. Arjen P. de Vries, Ph.D.: He received his Ph.D. in Computer Science from the University of Twente in 1999, on the integration of content management in database systems. He is especially interested in the new requirements on the design of database systems to support content-based retrieval in multimedia digital libraries. He has continued to work on multimedia database systems as a postdoc at the CWI in Amsterdam as well as University of Twente. Menzo Windhouwer: He received his MSc in Computer Science and Management from the University of Amsterdam in 1997. Currently he is working in the CWI Database Research Group on his Ph.D., which is concerned with multimedia indexing and retrieval using feature grammars. Peter M.G. Apers, Ph.D.: He is a full professor in the area of databases at the University of Twente, the Netherlands. He obtained his MSc and Ph.D. at the Free University, Amsterdam, and has been a visiting researcher at the University of California, Santa Cruz and Stanford University. His research interests are query optimization in parallel and distributed database systems to support new application domains, such as multimedia applications and WWW. He has served on the program committees of major database conferences: VLDB, SIGMOD, ICDE, EDBT. In 1996 he was the chairman of the EDBT PC. In 2001 he will, for the second time, be the chairman of the European PC of the VLDB. Currently he is coordinating Editor-in-Chief of the VLDB Journal, editor of Data & Knowledge Engineering, and editor of Distributed and Parallel Databases. Martin Kersten, Ph.D.: He received his PhD in Computer Science from the Vrije Universiteit in 1985 on research in database security, whereafter he moved to CWI to establish the Database Research Group. Since 1994 he is professor at the University of Amsterdam. Currently he is heading a department involving 60 researchers in areas covering BDMS architectures, datamining, multimedia information systems, and quantum computing. In 1995 he co-founded Data Distilleries, specialized in data mining technology, and became a non-executive board member of the software company Consultdata Nederland. He has published ca. 130 scientific papers and is member of the editorial board of VLDB journal and Parallel and Distributed Systems. He acts as a reviewer for ESPRIT projects and is a trustee of the VLDB Endowment board.     

Flexible and efficient IR using array databases

The Matrix Framework is a recent proposal by Information Retrieval (IR) researchers to flexibly represent information retrieval models and concepts in a single multi-dimensional array framework. We provide computational support for exactly this framework with the array database system SRAM (Sparse Relational Array Mapping), that works on top of a DBMS. Information retrieval models can be specified in its comprehension-based array query language, in a way that directly corresponds to the underlying mathematical formulas. SRAM efficiently stores sparse arrays in (compressed) relational tables and translates and optimizes array queries into relational queries. In this work, we describe a number of array query optimization rules. To demonstrate their effect on text retrieval, we apply them in the TREC TeraByte track (TREC-TB) efficiency task, using the Okapi BM25 model as our example. It turns out that these optimization rules enable SRAM to automatically translate the BM25 array queries into the relational equivalent of inverted list processing including compression, score materialization and quantization, such as employed by custom-built IR systems. The use of the high-performance MonetDB/X100 relational backend, that provides transparent database compression, allows the system to achieve very fast response times with good precision and low resource usage.     

Hydrophilic interaction chromatography-based high-throughput sample preparation method for N-glycan analysis from total human plasma glycoproteins

Many diseases are associated with changes in the glycosylation of plasma proteins. To search for glycan biomarkers, large sample sets have to be investigated for which high-throughput sample preparation and analysis methods are required. We here describe a 96 well plate-based high-throughput procedure for the rapid preparation of 2-aminobenzoic acid (2-AA) labeled N-glycans from 10 microL of human plasma. During this procedure, N-glycans are released from glycoproteins and subsequently labeled with 2-AA without prior purification. A hydrophilic interaction chromatography (HILIC)-based solid phase extraction method is then applied to isolate the 2-AA labeled N-glycans, which can be analyzed by MALDI-TOF-MS, HPLC with fluorescence detection, and CE-MS. The relative standard deviation for the intrabatch repeatability and the interbatch repeatability of the sample preparation method remained below 7% and below 9%, respectively, for all peaks observed by HPLC. Similar results were obtained with MALDI-TOF-MS, where 47 N-glycans could be measured consistently. The 2-AA labeled N-glycans were additionally analyzed by a CE-ESI-Q-TOF-MS method, which featured high resolution and mass accuracy, allowing the unambiguous determination of the N-glycan compositions. Up to four times, 96 human plasma samples can be handled in parallel, which, together with the versatility of the 2-AA label, makes this procedure very attractive for glycomics analysis of larger sample cohorts.     

Thin Functional Zeolite Layer Supported on Infrared Resonant Nano-Antennas for the Detection of Benzene Traces

Infrared absorption spectroscopy is a powerful analytical tool that enables the identification of molecular species. The sensitivity of this technique, that is strongly limited by the small absorption cross-section of molecular vibration, can be greatly improved by resonant interaction with nano-antennas via the surface-enhanced infrared absorption (SEIRA) mechanism. However, most of the examples of SEIRA concern solid-state molecular layers adsorbed on the nano-antennas, while the detection of gas traces still remains elusive due to the spatial extent of the near-field that is used to amplify the molecular vibrations resonantly. Here, a hybrid system composed of a plasmonic nano-antenna array coupled with nanosized zeolite coating for detection of volatile organic compounds in the near field of the resonators is demonstrated. The concerted action of the coating and the nano-antennas enabled the authors to detect record traces of benzene (25 ppb) within 10 min. This approach may ultimately allow the fabrication of a compact system for rapid detection of pharmaceutical and biocompounds with high sensitivity and high selectivity.     

Tenant Empowerment Through Innovative Tenures: An Analysis of Woonbron–Maasoevers’ Client's Choice Programme

According to the recent Housing Memorandum (MVROM, 2000 MVROM 2000 Mensen-Wensen-Wonen: wonen in de 21e eeuw [What people want, where people live: housing in the 21st century] The Hague Ministry of Housing, Spatial Planning and the Environment  [Google Scholar] ), Dutch housing associations are expected to actively improve the control of tenants over their dwellings and their living environment and offer them more possibilities to choose their own type of tenure. Before the publication of the Memorandum, associations had already developed various innovative types of tenure, for example fixed rent contracts, tenant maintenance programmes and different forms of sale with discounts and risk-reducing conditions. With the introduction of these tenures, associations aim to contribute to their social objectives by improving tenants' satisfaction with their dwellings and to improve the market position of their stock as well. Our paper discusses innovative types of tenure that have been developed by the Dutch housing associations and their benefits and risks for tenant and landlord. We focus on the ‘Client's Choice’ programme that has been developed by the association WoonbronMaasoevers, which is recognised as a front-runner in offering households a wide range of choice in tenure and which is also illustrative of many of the benefits and risks of the innovative tenures.

We conclude that many of the innovative tenures, including the Client's Choice programme, can contribute to tenant empowerment and freedom of choice. However, low-income households will mostly have to keep relying on (social) rented housing and other forms of empowerment. For the landlord, the Client's Choice programme has the benefit of increasing cash flow, which can be used for (social) housing investments. However, there are also substantial financial risks, concerning the rate of sales, the development of market values and the potential costs of having to buy back all the dwellings at the end of their economic lifespan. Thus, the implementation of the Client's Choice programme on a large scale should be accompanied by measures to control or provide for these risks.     

Attention-gated reinforcement learning of internal representations for classification

Animal learning is associated with changes in the efficacy of connections between neurons. The rules that govern this plasticity can be tested in neural networks. Rules that train neural networks to map stimuli onto outputs are given by supervised learning and reinforcement learning theories. Supervised learning is efficient but biologically implausible. In contrast, reinforcement learning is biologically plausible but comparatively inefficient. It lacks a mechanism that can identify units at early processing levels that play a decisive role in the stimulus-response mapping. Here we show that this so-called credit assignment problem can be solved by a new role for attention in learning. There are two factors in our new learning scheme that determine synaptic plasticity: (1) a reinforcement signal that is homogeneous across the network and depends on the amount of reward obtained after a trial, and (2) an attentional feedback signal from the output layer that limits plasticity to those units at earlier processing levels that are crucial for the stimulus-response mapping. The new scheme is called attention-gated reinforcement learning (AGREL). We show that it is as efficient as supervised learning in classification tasks. AGREL is biologically realistic and integrates the role of feedback connections, attention effects, synaptic plasticity, and reinforcement learning signals into a coherent framework.