Geert Monsieur

Cell_motility: a cross-platform, open source application for the study of cell motion paths

BackgroundMigration is an important aspect of cellular behaviour and is therefore widely studied in cell biology. Numerous components are known to participate in this process in a highly dynamic manner. In order to obtain a better insight in cell migration, mutants or drugs are used and their motive phenotype is then linked with the disturbing factors. One of the typical approaches to study motion paths of individual cells relies on fitting mean square displacements to a persistent random walk function. Since the numerous calculations involved often rely on diverse commercial software packages, the analysis can be expensive, labour-intensive and error-prone work. Additionally, due to the nature of algorithms employed the calculations involved are not readily reproducible without access to the exact software package(s) used.ResultsWe here present the cell_motility software, an open source Java application under the GNU-GPL license that provides a clear and concise analysis workbench for large amounts of cell motion data. Apart from performing the necessary calculations, the software also visualizes the original motion paths as well as the results of the calculations to help the user interpret the data. The application features an intuitive graphical user interface as well as full user and developer documentation and both source and binary files can be freely downloaded from the project website at http://genesis.UGent.be/cell_motility .ConclusionIn providing a free, open source software solution for the automated processing of cell motion data, we aim to achieve two important goals: labs can greatly simplify their data analysis pipeline as switching between different computational software packages becomes obsolete (thus reducing the chances for human error during data manipulation and transfer) and secondly, to provide scientists in the field with a freely available common platform to perform their analyses, enabling more efficient data quality control through peer reviewing.

Pregnant mothers with resolved anxiety disorders and their offspring have reduced heart rate variability: implications for the health of children.

Objective Active anxiety disorders have lasting detrimental effects on pregnant mothers and their offspring but it is unknown if historical, non-active, maternal anxiety disorders have similar effects. Anxiety-related conditions, such as reduced autonomic cardiac control, indicated by reduced heart rate variability (HRV) could persist despite disorder resolution, with long-term health implications for mothers and children. The objective in this study is to test the hypotheses that pregnant mothers with a history of, but not current anxiety and their children have low HRV, predicting anxiety-like offspring temperaments. Methods The participants in this case-control study consist of 56 women during their first trimester and their offspring (15 male, 29 female). Women had a history of an anxiety disorder (n=22) or no psychopathology (n=34) determined using the Mini-International Neuropsychiatric Interview. The main outcome measures were indices of autonomic cardiac control including root mean square of successive differences (RMSSD) and high frequency (HF) variability. Children’s fearfulness was also assessed using the Laboratory Temperament Assessment Battery (Lab-TAB)-Locomotor Version. Results HRV was lower in women and children in the past anxiety group compared to controls. HRV measures for mothers and children were positively correlated in the anxiety group only. In all children, low HRV measures at 2-4 months were associated with a higher chance of fearful behavior at 9-10 months. Conclusions Pregnant women with previous but not current anxiety and their children have low HRV. Children with low HRV tend to show more fearfulness. These findings have implications for identifying children at risk of anxiety disorders and point to possible underlying mechanisms of child psychopathology.

Coordinated Web Services Orchestration

In a business process execution language (BPEL) process definition the sequence of exchanged messages typically originates from the sequence of business process activities and from the need of coordination of those activities across the participants of the process. As such business concerns (e.g. the sequence of business process steps) are of en mixed with technical aspects (e.g. the sequence of coordination messages). In this article we present an architecture to separate business and technical concerns, which results in a clearer overview of the high-level business process and improves the flexibility and maintainability of the orchestration architecture. The described architecture depends on existing Web service standards. Different eventing and coordination specifications are discussed. The ultimate architecture is mainly based on the WS-Brokered Notification and WS-Coordination framework specifications.

Handling transactional business services

This article discusses the handling of transactional business services, which are service compositions that orchestrate and coordinate underlying services to process a high-level business activity. The main contribution made in this article is the presentation of the pattern TBS handler, which describes how one can implement a transactional business service (TBS). This pattern functions as an overview pattern for a complete pattern language that is outlined in the text. This pattern language provides the appropriate ingredients for the implementation of a TBS. It is presented using thumbnails.

A pattern language for service input data provisioning

A common practice in service-orientation is the creation of a composite service by combining a set of other services. As discussed in this article, the orchestration of services to construct a new service requires several service interactions. This is why the construction of a composite service can be a complex and time-consuming task. Some services in a service composition can have the role of providing other services with (additional) input data. The pattern language in this article can help to design the service interactions that are needed for provisioning input data.

On the Concept of Service Coordination

In this research report we study service coordination, which is a crucial aspect when services are combined into service-based systems (Metzger & Pohl, 2009).Coordination is not only in computer science an important research topic. It is also studied in disciplines such as organization theory, operations research, economics, linguistics, and psychology. Malone & Crowston (1994) studied the similarities and connections between the different flavors of coordination and created a more generic coordination theory. They define coordination as managing dependencies between activities. This definition is based on the intuitive idea that there is nothing to coordinate without any interdependence. In their work they state that coordination theories should try to characterize different kinds of dependencies and identify the coordination processes that can be used to manage them. Therefore, in the next section (see Section 2), we will discuss several types of dependencies that can exist when composing services to service-based systems. In the rest of this research report is targeted at two types of dependencies, namely sequence dependencies and data dependencies. Therefore, the research continues in Sections 3 and 4 with an overview of existing techniques for managing sequence and data dependencies, respectively. In each section there is also a general conclusion included.

Web Services Specifications on Eventing and Coordination

The WS-Events specification consists of ‘a set of processing rules for advertising, subscribing, producing and consuming Web services Events’. All authors of this specification are based at Hewlett-Packard. Further development of WS-Events is not on the agenda anymore. Therefore we only give a brief overview of this specification.WS-Events defines an event as a change in the state of a resource or request for processing. The specification describes three main entities. The event producer is an entity which generates notifications. These notifications are received by the event consumers. The event broker is responsible for routing the notifications. Brokers typically aggregate and publish events from several producers. An event broker can also apply some transformation to the notifications it processes. The precise role of the broker remains unclear in WS-events. Subscription requests and notifications are described as (direct) messages between the event producer and the event consumer.The specification does not provide descriptions of entities responsible for subscription or subscription management tasks (such as the subscriber and subscription manager in WS-Notification and WS-Eventing) nor does it distinguish between publisher and producer roles (as in WS-Brokered Notification).The WS-Eventing specification describes a protocol that allows Web services to subscribe to or accept subscriptions for event notification messages. The specification defines four entities in the event notification architecture