Enabling a direct path from end-user specifications to executable protocols in a biology laboratory environment

Biomedical analyses are becoming increasingly complex, with respect to both the type of the data to be produced and the procedures to be executed. This trend is expected to continue in the future. The development of information and protocol management systems that can sustain this challenge is therefore becoming an essential enabling factor for all actors in the field. The use of custom-built solutions that require the biology domain expert to acquire or procure software engineering expertise in the development of the laboratory infrastructure is not fully satisfactory because it incurs undesirable mutual knowledge dependencies between the two camps. We propose instead an infrastructure concept that enables the domain experts to express laboratory protocols using proper domain knowledge, free from the incidence and mediation of the software implementation artefacts. In the system that we propose this is made possible by basing the modelling language on an authoritative domain specific ontology and then using modern model-driven architecture technology to transform the user models in software artefacts ready for execution in a multi-agent based execution platform specialized for biomedical laboratories.

Evaluation der Langzeitcompliance lebertransplantierter Patienten mit der immunsuppressiven Therapie und eines Betreuungsmodells zur intersektoralen kooperativen pharmazeutischen Betreuung durch eine Krankenhausapotheke und öffentliche Apotheken

Ein wichtiger Baustein für den langfristigen Erfolg einer Lebertransplantation ist die Compliance mit der lebenslang einzunehmenden immunsuppressiven Therapie. Im Rahmen der vorliegenden Arbeit wurde erstmals mittels MEMS® die Compliance bei lebertransplantierten Patienten untersucht, deren Transplantation einige Jahre zurücklag. Rekrutiert wurden Patienten, die vor 2, 5, 7 oder 10 Jahren (Gruppe 2 y.p.t., 5 y.p.t., 7 y.p.t., 10 y.p.t.) in der Universitätsmedizin Mainz lebertransplantiert wurden. 39 Patienten nahmen an der prospektiven Anwendungsbeobachtung teil. Die Compliance wurde mittels MEMS® über eine Beobachtungszeit von 6 Monaten erfasst. Bei der MEMS®-Auswertung war zu vermuten, dass 10 Patienten diese nicht wie vorgesehen verwendet hatten. Folglich konnten die mittels MEMS® gemessenen Compliance-Parameter nur für 29 Patienten valide ermittelt werden. Die mittlere Dosing Compliance betrug 81 ± 21 %, wobei die Gruppe 2 y.p.t. mit 86 ± 14 % bessere Werte zu verzeichnen hatte als die Gruppe 5 y.p.t. (75 ± 27 %) und 7 y.p.t. (74 ± 28 %). Die Ergebnisse waren jedoch nicht signifikant unterschiedlich (p=0,335, Kruskal-Wallis-Test). Unter Einbeziehung aller mittels MEMS® gemessenen Compliance-Parameter wurden 19 von 29 Patienten (66 %) als compliant eingestuft. Bei der Analyse der Gesamtcompliance basierend auf den subjektiven Compliance-Messmethoden (Morisky-Fragebogen, MESI-Fragebogen, Selbsteinschätzung), der Arzneimittel-Blutspiegel und der Anzahl an Abstoßungsreaktionen, in der alle 39 Patienten einbezogen werden konnten, wurden 35 Patienten (90 %) als compliant eingestuft. rnIm zweiten Teil der Arbeit wurde die Etablierung und Bewertung eines intersektoralen Pharmazeutischen Betreuungskonzepts für lebertransplantierte Patienten untersucht. Erstmals wurden anhand eines entwickelten schnittstellenübergreifenden, integrierten Betreuungskonzepts niedergelassene Apotheker in die Pharmazeutische Betreuung lebertransplantierter Patienten eingebunden. 20 Patienten wurden rekrutiert und während ihres stationären Aufenthaltes nach Transplantation pharmazeutisch betreut. Die Betreuung umfasste eine intensive Patientenschulung mit drei bis vier Gesprächen durch einen Krankenhausapotheker. Während des stationären Aufenthaltes wurden arzneimittelbezogene Probleme erkannt, gelöst und dokumentiert. Bei Entlassung stellte der Krankenhausapotheker einen Medikationsplan für den Hausarzt sowie für den niedergelassenen Apotheker aus und führte mit den Patienten ein ausführliches Entlassungsgespräch. Darüber hinaus wurden den Patienten Arzneimitteleinnahmepläne und eine Patienteninformation über ihr immunsuppressives Arzneimittel übergeben. 15 Patienten konnten daraufhin ambulant von niedergelassenen Apothekern pharmazeutisch weiterbetreut werden. Das kooperierende pharmazeutische Personal wurde durch ein eigens für die Studie erstelltes Manual zur Pharmazeutischen Betreuung lebertransplantierter Patienten geschult und unterstützt. Die niedergelassenen Apotheker sollten die Patienten in ihrer Arzneimitteltherapie begleiten, indem Beratungsgespräche geführt und arzneimittelbezogene Probleme erkannt und gelöst wurden. Die Nutzeffekte der intensiven Pharmazeutischen Betreuung konnte anhand verschiedener Erhebungsinstrumente dargelegt werden. Im Ergebnis resultierte eine hohe Zufriedenheit der Patienten und Apotheker mit dem Betreuungskonzept, die mittels Selbstbeurteilungsfragebögen ermittelt wurde. Die Compliance der Patienten wurde anhand des Morisky- und MESI-Fragebogens, der Selbsteinschätzung der Patienten, Blutspiegelbestimmungen sowie der Einschätzung durch den niedergelassenen Apotheker bestimmt. 86 % der Patienten wurden als compliant eingeordnet. Die Kenntnisse der Patienten über ihre immunsuppressive Therapie, welche anhand von Interviews erfragt wurden, lagen auf einem sehr hohen Niveau. Abschließend kann festgestellt werden, dass die Pharmazeutische Betreuung lebertransplantierter Patienten in den niedergelassenen Apotheken durchführbar ist. Anhand der Dokumentationsprotokolle lässt sich allerdings nur sehr schwer beurteilen, in welchem Maße die Betreuung tatsächlich erfolgte. Das tatsächliche vorliegen einer mangelnden Betreuung oder aber eine lückenhafte Dokumentation der Betreuungsleistung war nicht zu differenzieren. Ein limitierender Faktor für die intensivierte Betreuung ist sicherlich der erhebliche Aufwand für nur einen Patienten mit einem seltenen Krankheitsbild. Das Erkennen und Lösen von 48 ABP durch den Krankenhausapotheker und 32 ABP durch die niedergelassenen Apotheker, d. h. insgesamt 4,5 ABP pro Patient zeigt, dass die Pharmazeutische Betreuung einen wichtigen Beitrag für eine qualitätsgesicherte Arzneimitteltherapie leistet. Die intersektorale Pharmazeutische Betreuung stellt eine wesentliche Hilfe und Unterstützung der Patienten im sicheren Umgang mit ihrer Arzneimitteltherapie dar.rn

Application Platforms for the Internet of Things: Theory, Architecture, Protocols, Data Formats, and Privacy

The Internet of Things (IoT) is the next industrial revolution: we will interact naturally with real and virtual devices as a key part of our daily life. This technology shift is expected to be greater than the Web and Mobile combined. As extremely different technologies are needed to build connected devices, the Internet of Things field is a junction between electronics, telecommunications and software engineering. Internet of Things application development happens in silos, often using proprietary and closed communication protocols. There is the common belief that only if we can solve the interoperability problem we can have a real Internet of Things. After a deep analysis of the IoT protocols, we identified a set of primitives for IoT applications. We argue that each IoT protocol can be expressed in term of those primitives, thus solving the interoperability problem at the application protocol level. Moreover, the primitives are network and transport independent and make no assumption in that regard. This dissertation presents our implementation of an IoT platform: the Ponte project. Privacy issues follows the rise of the Internet of Things: it is clear that the IoT must ensure resilience to attacks, data authentication, access control and client privacy. We argue that it is not possible to solve the privacy issue without solving the interoperability problem: enforcing privacy rules implies the need to limit and filter the data delivery process. However, filtering data require knowledge of how the format and the semantics of the data: after an analysis of the possible data formats and representations for the IoT, we identify JSON-LD and the Semantic Web as the best solution for IoT applications. Then, this dissertation present our approach to increase the throughput of filtering semantic data by a factor of ten.

Mac protocols for linear wireless (sensor) networks

Wireless sensor networks (WSNs) consist of a large number of sensor nodes, characterized by low power constraint, limited transmission range and limited computational capabilities [1][2].The cost of these devices is constantly decreasing, making it possible to use a large number of sensor devices in a wide array of commercial, environmental, military, and healthcare fields. Some of these applications involve placing the sensors evenly spaced on a straight line for example in roads, bridges, tunnels, water catchments and water pipelines, city drainages, oil and gas pipelines etc., making a special class of these networks which we define as a Linear Wireless Network (LWN). In LWNs, data transmission happens hop by hop from the source to the destination, through a route composed of multiple relays. The peculiarity of the topology of LWNs, motivates the design of specialized protocols, taking advantage of the linearity of such networks, in order to increase reliability, communication efficiency, energy savings, network lifetime and to minimize the end-to-end delay [3]. In this thesis a novel contention based Medium Access Control (MAC) protocol called L-CSMA, specifically devised for LWNs is presented. The basic idea of L-CSMA is to assign different priorities to nodes based on their position along the line. The priority is assigned in terms of sensing duration, whereby nodes closer to the destination are assigned shorter sensing time compared to the rest of the nodes and hence higher priority. This mechanism speeds up the transmission of packets which are already in the path, making transmission flow more efficient. Using NS-3 simulator, the performance of L-CSMA in terms of packets success rate, that is, the percentage of packets that reach destination, and throughput are compared with that of IEEE 802.15.4 MAC protocol, de-facto standard for wireless sensor networks. In general, L-CSMA outperforms the IEEE 802.15.4 MAC protocol.

Dental arch relationship in children with complete unilateral cleft lip and palate following one-stage and three-stage surgical protocols

The objective of this study is to compare dental arch relationship following one-stage and three-stage surgical protocols of unilateral cleft lip and palate. Dental casts of 61 children (mean age, 11.2 years; SD, 1.7), consecutively treated in one center with one-stage closure of the complete cleft at 9.2 months (SD, 2.0), were compared with a sample of 97 patients (mean age, 8.7 years; SD, 0.9), consecutively treated with a three-stage protocol including delayed hard palate closure in another center. The dental casts were assigned random numbers to blind their origin. Four raters graded dental arch relationship and palatal morphology using the EUROCRAN index. The strength of agreement of rating was assessed with kappa statistics. Independent t tests were run to compare the EUROCRAN scores between one-stage and three-stage samples, and Fisher's exact tests were performed to evaluate differences of distribution of the EUROCRAN grades. The intra- and inter-rater agreement was moderate to very good. Dental arch relationship in the one-stage sample was less favorable than in three-stage group (mean scores, 2.58 and 1.97 for one-stage and three-stage samples, respectively; p?

Posttraumatic stress disorder and soluble cellular adhesion molecules at rest and in response to a trauma-specific interview in patients after myocardial infarction

Posttraumatic stress disorder (PTSD) and circulating cellular adhesion molecules (CAMs) predict cardiovascular risk. We hypothesized a positive relationship between PTSD caused by myocardial infarction (MI) and soluble CAMs. We enrolled 22 post-MI patients with interviewer-rated PTSD and 22 post-MI patients with no PTSD. At 32±6months after index MI, all patients were re-scheduled to undergo the Clinician-Administered PTSD Scale (CAPS) interview and had blood collected to assess soluble CAMs at rest and after the CAPS interview. Relative to patients with no PTSD, those with PTSD had significantly higher levels of soluble vascular cellular adhesion molecule (sVCAM)-1 and intercellular adhesion molecule (sICAM)-1 at rest and, controlling for resting CAM levels, significantly higher sVCAM-1 and sICAM-1 after the interview. Greater severity of PTSD predicted significantly higher resting levels of sVCAM-1 and soluble P-selectin in patients with PTSD. At follow-up, patients with persistent PTSD (n=15) and those who had remitted (n=7) did not significantly differ in CAM levels at rest and after the interview; however, both these groups had significantly higher sVCAM-1 and sICAM-1 at rest and also after the interview compared to patients with no PTSD. Elevated levels of circulating CAMs might help explain the psychophysiologic link of PTSD with cardiovascular risk.

Momentary stress moderates procoagulant reactivity to a trauma-specific interview in patients with posttraumatic stress disorder caused by myocardial infarction

Hypercoagulability of the blood might partially explain the increased cardiovascular disease risk in posttraumatic stress disorder (PTSD) and is also triggered by anticipatory stress. We hypothesized exaggerated procoagulant reactivity in patients with PTSD in response to a trauma-specific interview that would be moderated by momentary stress levels. We examined 23 patients with interviewer-diagnosed PTSD caused by myocardial infarction (MI) and 21 post-MI patients without PTSD. A second diagnostic (i.e., trauma-specific) interview to assess posttraumatic stress severity was performed after a median follow-up of 26 months (range 12-36). Before that interview patients rated levels of momentary stress (Likert scale 0-10) and had blood collected before and after the interview. The interaction between PTSD diagnostic status at study entry and level of momentary stress before the follow-up interview predicted reactivity of fibrinogen (P=0.036) and d-dimer (P=0.002) to the PTSD interview. Among patients with high momentary stress levels, PTSD patients had greater fibrinogen (P=0.023) and d-dimer (P=0.035) reactivity than non-PTSD patients. Among patients with low momentary stress levels, PTSD patients had less d-dimer reactivity than non-PTSD patients (P=0.024); fibrinogen reactivity did not significantly differ between groups. Momentary stress levels, but not severity of posttraumatic stress, correlated with d-dimer reactivity in PTSD patients (r=0.46, P=0.029). We conclude that momentary stress levels moderated the relationship between PTSD and procoagulant reactivity to a trauma-specific interview. Procoagulant reactivity in post-MI patients with PTSD confronted with their traumatically experienced MI was observed if patients perceived high levels of momentary stress before the interview.

Delivery room management of very low birth weight infants in Germany, Austria and Switzerland--a comparison of protocols

Surveys from the USA, Australia and Spain have shown significant inter-institutional variation in delivery room (DR) management of very low birth weight infants (VLBWI, <1500g) at birth, despite regularly updated international guidelines.