Protocol-Safe Workflow Support for Santa Claus

Practical software analysis techniques exploit a form a process description, mostly in some \ud avour of state diagram. Unlike typing information, these process structures are usually not passed down to the implementation level, and neither are they exploited in any form of consistency check. It is our belief that the information in most designs suffices to perform all sorts of consistency checks. This workshop paper studies a simple case where work\ud ow processes interact with `actual' objects at the implementation level, and demonstrates how useful protocol checking can be in making and keeping these processes consistent with each other

On Practical Verification of Processes

The integration of a formal process theory with a practically usable notation is not straightforward, but it is necessary for practical verification of process specifications. Given such an intermediate language, a verification process that gives useful feedback is not trivial either: Model checkers are not powerful enough to deal with object models, and theorem provers provide insu#cient feedback and are not certain to find a proof

Applications of Research Data Management at GESIS Data Archive for the Social Sciences

The chapter "Applications of Research Data Management at GESIS Data Archive for the Social Sciences" explores ways in which an archive - i.e. an organization whose work has a strong focus on preservation and dissemination of digital data - can become involved in research data management (RDM). The Data Archive looks back on a long history of working with researchers to make their data re-usable and accessible since 1960. Today it provides support for Research Data Management across the entire data lifecycle by offering a wide range of tools and services tailored to the needs of different types of stakeholders. The chapter gives an overview of selected tools and services offered in the areas of metadata and data documentation, data preparation, data publication, and long-term preservation. To illustrate how support for research data management plays out in different settings, three case studies for typical scenarios are presented: 1) The European Values Survey (EVS), a large international longitudinal survey studying basic human values across Europe. 2) The German Longitudinal Election Study (GLES), a national survey program with a comprehensive approach to gain insights into the German federal elections. 3) A data center in the health sector which decided to make data originally collected to support policy-making available to research

Spartan Daily, December 9, 1997

Volume 109, Issue 68https://scholarworks.sjsu.edu/spartandaily/9215/thumbnail.jp

Improved approaches to ligand growing through fragment docking and fragment-based library design

Die Fragment-basierte Wirkstoffforschung (“fragment-based drug discovery“ – FBDD) hat in den vergangenen zwei Jahrzehnten kontinuierlich an Beliebtheit gewonnen und sich zu einem dominanten Instrument der Erforschung neuer chemischer Moleküle als potentielle bioaktive Modulatoren entwickelt. FBDD ist eng mit Ansätzen zur Fragment-Erweiterung, wie etwa dem Fragment-„growing“, „merging“ oder dem „linking“, verknüpft. Diese Entwicklungsansätze können mit Hilfe von Computerprogrammen oder teilautomatischen Prozessen der „de novo“ Wirkstoffentwicklung beschleunigt werden. Obwohl Computer mühelos Millionen von Vorschlägen generieren können, geschieht dies allerdings oft auf Kosten unsicherer synthetischer Realisierbarkeit der Verbindungen mit einer potentiellen Sackgasse im Optimierungsprozess. Dieses Manuskript beschreibt die Entwicklung zweier computerbasierter Instrumente, PINGUI und SCUBIDOO, mit dem Ziel den FBDD Ausarbeitungs-Zyklus zu fördern. PINGUI ist ein halbautomatischer Arbeitsablauf zur Fragment-Erweiterung basierend auf der Proteinstruktur unter Berücksichtigung der synthetischen Umsetzbarkeit. SCUBIDOO ist eine freizugängliche Datenbank mit aktuell 21 Millionen verfügbaren virtuellen Produkten, entwickelt durch die Kombination kommerziell verfügbarer Bausteine („building blocks“) mit bewährten organischen Reaktionen. Zu jedem erzeugten virtuellen Produkt wird somit eine Synthesevorschrift geliefert. Die entscheidenden Funktionen von PINGUI, wie die Erzeugung abgeleiteter Bibliotheken oder das Anwenden organischer Reaktionen, wurden daraufhin in die SCUBIDOO Webseite integriert. PINGUI als auch SCUBIDOO wurden des Weiteren zur Erforschung Fragment-basierter Liganden („fragment-based ligand discovery“) mit dem β-2 adrenergen Rezeptor (β-2-AR) und der PIM1 Kinase als Zielproteine („targets“) eingesetzt. Im Rahmen einer ersten Studie zum β-2-AR wurden mit PINGUI acht unterschiedliche Erweiterungen für verschiedene Fragment-Treffer („hits“) vorhergesagt (ausgewählt?). Alle acht Verbindungen konnten dabei erfolgreich synthetisiert werden und vier der acht Produkte zeigten im Vergleich zu den Ausgangsfragmenten eine erhöhte Affinität zum target. Eine zweite Studie umfasste die Anwendung von SCUBIDOO zur schnellen Identifikation von Fragmenten und deren möglichen Erweiterungen mit potentieller Bindungsaktivität zur PIM-1 Kinase. Als Ergebnis ergab sich ein Fragment-Treffer mit der dazugehörigen Kristallstruktur. Weitere Folgeprodukte befinden sich derzeit in Synthese. Abschließend wurde SCUBIDOO an eine automatische Roboter- Synthese gekoppelt, wodurch hunderte von Verbindungen effizient parallel synthetisiert werden können. 127 der 240 vorhergesagten Produkte (53%) wurden mit dem Ziel an den β-2-AR zu binden bereits synthetisiert und werden in Kürze weitergehend getestet. Die beiden vorgestellten Computer-Tools könnten zur Verbesserung im Anfangsstadium befindlicher Projekte zur Fragment-basierten Wirkstoffentwicklung, vor allem hinsichtlich der Strategien im Bereich der Fragment Erweiterung, eingesetzt werden. PINGUI zum Beispiel generiert Vorschläge zur Fragment- Erweiterung, die sich mit hoher Wahrscheinlichkeit an die Zielstruktur anlagern, und stellt somit ein nützliches und kreatives Werkzeug zur Untersuchung von Struktur-Wirkungsbeziehungen („structure-activity relationship“ – SAR) dar. SCUBIDOO zeigte sich mit einem bisherigen 53-prozentigen Synthese-Erfolg als zugänglich für die Integration an die effiziente automatisierte Roboter-Synthese. Jede zukünftige Synthese liefert neue Kenntnisse innerhalb der Datenbank und wird somit nach und nach den Synthese-Erfolg erhöhen. Des Weiteren stellen alle synthetisierten Produkte neuartige Verbindungen dar, was umso mehr den möglichen Einfluss SCUBIDOOs bei der Entdeckung neuer chemischer Strukturen hervorhebt

Guidelines for TMS/tES Clinical Services and Research through the COVID-19 Pandemic

BACKGROUND: The COVID-19 pandemic has broadly disrupted biomedical treatment and research including non-invasive brain stimulation (NIBS). Moreover, the rapid onset of societal disruption and evolving regulatory restrictions may not have allowed for systematic planning of how clinical and research work may continue throughout the pandemic or be restarted as restrictions are abated. The urgency to provide and develop NIBS as an intervention for diverse neurological and mental health indications, and as a catalyst of fundamental brain research, is not dampened by the parallel efforts to address the most life-threatening aspects of COVID-19; rather in many cases the need for NIBS is heightened including the potential to mitigate mental health consequences related to COVID-19. OBJECTIVE: To facilitate the re-establishment of access to NIBS clinical services and research operations during the current COVID-19 pandemic and possible future outbreaks, we develop and discuss a framework for balancing the importance of NIBS operations with safety considerations, while addressing the needs of all stakeholders. We focus on Transcranial Magnetic Stimulation (TMS) and low intensity transcranial Electrical Stimulation (tES) - including transcranial Direct Current Stimulation (tDCS) and transcranial Alternating Current Stimulation (tACS). METHODS: The present consensus paper provides guidelines and good practices for managing and reopening NIBS clinics and laboratories through the immediate and ongoing stages of COVID-19. The document reflects the analysis of experts with domain relevant expertise spanning NIBS technology, clinical services, and basic and clinical research - with an international perspective. We outline regulatory aspects, human resources, NIBS optimization, as well as accommodations for specific demographics. RESULTS: A model based on three phases (early COVID-19 impact, current practices, and future preparation) with an 11-step checklist (spanning removing or streamlining in-person protocols, incorporating telemedicine, and addressing COVID-19-associated adverse events) is proposed. Recommendations on implementing social distancing and sterilization of NIBS related equipment, specific considerations of COVID-19 positive populations including mental health comorbidities, as well as considerations regarding regulatory and human resource in the era of COVID-19 are outlined. We discuss COVID-19 considerations specifically for clinical (sub-)populations including pediatric, stroke, addiction, and the elderly. Numerous case-examples across the world are described. CONCLUSION: There is an evident, and in cases urgent, need to maintain NIBS operations through the COVID-19 pandemic, including anticipating future pandemic waves and addressing effects of COVID-19 on brain and mind. The proposed robust and structured strategy aims to address the current and anticipated future challenges while maintaining scientific rigor and managing risk

Biodiversity and Biocollections: Problem of Correspondence

This text is an English translation of those several sections of the original paper in Russian, where collection-related issues are considered. The full citation of the original paper is as following: Pavlinov I.Ya. 2016. [Bioraznoobrazie i biokollektsii: problema sootvetstvia]. In: Pavlinov I.Ya. (comp.). Aspects of Biodiversity. Archives of Zoological Museum of Lomonosov Moscow State University, Vol. 54, Pр. 733–786. Orientation of biology, as a natural science, on the study and explanation of the similarities and differences between organisms led in the second half of the 20th century to the recognition of a specifi c subject area of biological explorations, viz. biodiversity (BD). One of the important general scientifi c prerequisites for this shift was understanding that (at the level of ontology) the structured diversity of the living nature is its fundamental property equivocal to subjecting of some of its manifestations to certain laws. At the level of epistemology, this led to acknowledging that the “diversifi cationary” approach to description of the living beings is as justifi able as the before dominated “unifi cationary” one. This general trend has led to a signifi cant increase in the attention to BD. From a pragmatic perspective, its leitmotif was conservation of BD as a renewable resource, while from a scientifi c perspective the leitmotif was studying it was studying BD as a specifi c natural phenomenon. These two points of view are united by recognition of the need for scientific substantiation of BD conservation strategy, which implies the need for a detailed study of BD itself. At the level of ontology, one of the key problems in the study of BD (leaving aside the question of its genesis) is determination of its structure, which is interpreted as a manifestation of the structure of the Earth’s biota itself. With this, it is acknowledged that the subject area of empirical explorations is not the BD as a whole ( “Umgebung”) but its particular manifestations (“Umwelts”). It is proposed herewith to recognized, within the latter: fragments of BD (especially taxa and ecosystems), hierarchical levels of BD (primarily within- and interorganismal ones), and aspects of BD (before all taxonomic and meronomic ones). Attention is drawn to a new interpretation of bioinformatics as a discipline that studies the information support of BD explorations. An important fraction of this support are biocollections. The scientifi c value of collections means that they make it possible both empirical inferring and testing (verification) of the knowledge about BD. This makes biocollections, in their epistemological status, equivalent to experiments, and so makes studies of BD quite scientific. It is emphasized that the natural objects (naturalia), which are permanently kept in collections, contain primary (objective) information about BD, while information retrieved somehow from them is a secondary (subjective) one. Collection, as an information resource, serves as a research sample in the studies of BD. Collection pool, as the totality of all collection materials kept in repositories according to certain standards, can be treated as a general sample, and every single collection as a local sample. The main characteristic of collection-as-sample is its representativeness; so the basic strategy of development of the collection pool is to maximize its representativeness as a means to ensure correspondence of structure of biocollection pool to that of BD itself. The most fundamental characteristic of collection, as an information resource, is its scientific signifi cance. The following three main groups of more particular characteristics are distinguished: — the “proper” characteristics of every collection are its meaningfulness, informativeness, reliability, adequacy, documenting, systematicity, volume, structure, uniqueness, stability, lability; — the “external” characteristics of collection are resolution, usability, ethic constituent; — the “service” characteristics of collection are its museofication, storage system security, inclusion in metastructure, cost. In the contemporary world, development of the biocollection pool, as a specific resource for BD research, requires considerable organizational efforts, including work on their “information support” aimed at demonstrating the necessity of existence of the biocollections