Search

The experimental capabilities at the MAX IV synchrotron consists of 17 beamlines at full capacity. Each beamline puts different requirements on the control system in terms of data acquisition, high performance, data volume, pre-processing needs, and fast experiment feedback and online visualization. Therefore, high demands are put on the data management systems, and the reliability and performance of these systems has a big impact on the overall success of the facility. At MAX IV we have started the DataStaMP (Data Storage and Management Project) with the aim of providing a unified and reliable solution for all data sources in our facility. This work presents the control system aspects of the project. It is initially aimed at providing data management solution for a selected number of detectors and beamlines. It is developed in a modular and scalable architecture and combines several programming languages and frameworks. All the software runs in a dedicated cluster and communicates with the experimental stations through high performance networks, using gRPC to talk to the control system and ZMQ for retrieving the data stream., Proceedings of the 17th International Conference on Accelerator and Large Experimental Physics Control Systems, ICALEPCS2019, New York, NY, USA

MAX IV Laboratory, inaugurated in June 2016, has for the last 8 months accepted synchrotron users on three beamlines, NanoMAX, BioMAX and Hippie, while simultaneously pushing towards bringing more beamlines into the commissioning and user phases. As evidence of this, the last call issued addressed 10 beamlines. As of summer 2019, MAX IV has reached a point where 11 beamlines simultaneously have shutters open and are thus receiving light under stable operation. With 16 beamlines funded, the number of beamlines will grow over the coming years. The Controls and IT group has performed numerous beamline system installations such as a sample changer at BioMAX, Dectris detector at Nanomax, and End Station at Hippie. It has additionally developed processes, such as automated IT infrastructure with a view to accepting users. We foresee a focus on end stations and detectors, as well as data storage, data handling and scientific software. As an example, a project entitled "DataStaMP" has been recently funded aiming to increase the data and metadata storage and management system in order to accommodate the ever increasing demand for storage and access., Proceedings of the 17th International Conference on Accelerator and Large Experimental Physics Control Systems, ICALEPCS2019, New York, NY, USA

Users visiting scientific installations aim to collect the best quality data frequently under time pressure. They look for complementary techniques at different sites and when they arrive to one they have limited time to understand the data acquisition architecture. In these conditions, the availability of generic and common interfaces to the experimental channels and measurements improve the user experience regarding the programming and configuration of the experiment. Here we present solutions to the data acquisition challenges provided by the Sardana scientific SCADA suite. In one experimental session the same detector may be employed in different modes e.g., getting the data stream when aligning the sample or the stage, getting a single time/monitor controlled exposure and finally running the measurement process like a step or continuous scan. The complexity of the acquisition setup increases with the number of detectors being simultaneously used and even more depending on the applied synchronization. In this work we present recently enriched Sardana interfaces and optimized processes and conclude with the roadmap of further enhancements., Proceedings of the 17th International Conference on Accelerator and Large Experimental Physics Control Systems, ICALEPCS2019, New York, NY, USA

Laura Khurana,1 Ellen M Durand,1 Sarah Tressel Gary,1 Antonio V Otero,1 Kelly M Dumais,1 Jamie Beck,1 David Zurakowski,2 Christine Teel Hall,1 Susan M Dallabrida11eResearch Technology (ERT), Boston, MA, USA; 2Harvard Medical School, Boston Children’s Hospital, Boston, MA, USAPurpose: Effective health care and patient adherence to their prescribed regimens relies on successful communication between patients and their providers. This study examined mechanisms for optimizing patient–physician communication in subjects with type 2 diabetes, with a focus on optimizing the incorporation of e-clinical technology to improve engagement and communication.Methods: A total of 105 subjects with type 2 diabetes participating in a large US mode equivalency study were surveyed independently of this trial. In addition to demographic information, each subject was queried on their familiarity with and preference for e-clinical technologies. Survey questions focused on mobile technology use, perceptions, and preferences for improving communication and interactions with health care providers.Results: Subjects were diverse in age, sex, education, and ethnicity. Forty nine percent owned a smartphone, and 64% had a computer at home. Most subjects (81%) were interested in using electronic methods (eg, app on a smartphone, email, or text messages) to interact more with physicians between visits. The majority of subjects were interested in using technology to help manage their type 2 diabetes, including 62% favoring communicating with their health-care providers via email and a considerable fraction interested in using smartphones to be provided medication reminders (56%), clinical visit scheduling (55%), and text messaging (49%).Conclusion: Subjects are interested in using electronic methods to increase communication with their physicians and manage their type 2 diabetes. Health-care providers should consider engaging patients with e-clinical technology to increase patient–physician communication and for the ultimate goal of improved health care.Keywords: technology, eCOA, preferences, electronic, smartphone

We present evidence that quantitative definitions of extreme events in wind, so called gusts, may be flawed and unable to grasp true extreme situations of wind velocity in short time intervals. In particular, we show that the same statistics of particular pattern shapes in wind data are found in surrogate data generated from the original series of measurements. We apply a pattern recognition algorithm to a two-parameter “Mexican-hat” (duration and amplitude) and find the same probability of occurrence for both original measurements and surrogate data. The distribution of the corresponding values of the duration and amplitude present deviations that can be explained by the filtering of n-point correlations in the original series.

Leukemia is a type of cancer that starts in blood-forming tissue, such as the bone marrow. It causes the production of large numbers of abnormal blood cells that end up entering into the bloodstream. Within the different types of leukemia, Mantle Cell Lymphoma (MCL) is the one with the worst prognosis due to the short survival average of a patient, which is close to three years. This tumor is characterized by the over-expression of Cyclin D1, a protein that helps control cell division. MCL is also characterized by the binding of this protein to certain regions of DNA involved in the regulation of DNA-damage response (DDR). The presented study aims to identify similarities between the gene expression regulated by Cyclin D1 in lymphomas and the gene expression in DNA damage. That knowledge will allow the exploration of essential mechanisms of carcinogenesis and help in the identification of genes that could be an interesting therapeutic target in the process of tumor progression. Additionally, new biomarkers that could be used in early diagnosis can be found. With the addition of machine learning algorithms to the biology analysis pipeline, this project explores new ways to improve the traditional methodologies and boost the identification of significantly enriched genes that will serve the purposes mentioned above. The result of such a pipeline is the accurate selection of genes correlated with Cyclin D1, involved in MCL and DDR, and its posterior analysis and identification of significantly enriched gene sets. As a conclusion, the results obtained in this study suggested that targeting of Notch pathway and studying potential common mechanisms of hypoxia and apoptosis resistance would be of great interest for possible future studies on treatments of MCL. La leucemia es un tipo de cáncer que empieza en los tejidos generadores de sangre, tales como la médula ósea. Esta enfermedad causa la producción de un gran número de células sanguíneas anormales que van a parar al flujo sanguíneo. Dentro de la leucemia encontramos diferentes tipos, siendo el Linfoma de las células del manto (en adelante, Mantle Cell Lymphoma o MCL) el que peor pronóstico tiene, debido a la corta media de supervivencia del paciente, cercana a los tres años. Este tumor se caracteriza por la sobre-expresión de la ciclina D1, proteína que ayuda a controlar la división celular, y también por la unión de ésta proteína a ciertas regiones de ADN involucradas en la regulación del proceso de reparación del daño al ADN (en adelante, DNA-Damage Response o DDR). El presente estudio tiene como objetivo identificar las similitudes entre la expresión génica derivada de la regulación por la ciclina D1 en Linfoma con la que se da en el caso del daño en el ADN. Este conocimiento permitirá la exploración de los mecanismos esenciales de carcinogénesis y ayudará en la identificación de genes que pueden ser un objetivo terapéutico interesante en el proceso de progresión tumoral. Adicionalmente, se podrían hallar nuevos biomarcadores para el diagnóstico precoz de la enfermedad. Con la adición de machine learning al proceso de análisis biológico, este proyecto explora nuevas formas de mejorar las metodologías tradicionales e impulsar la identificación de genes significativamente enriquecidos que servirán a los propósitos mencionados anteriormente. El resultado de dicho proceso analítico es la precisa selección de genes correlacionados con la ciclina D1, involucrados en MCL y DDR, y su posterior análisis. Como conclusión, los resultados obtenidos en este estudio sugirieron que el tratamiento del Notch pathway y el potencial estudio de los mecanismos comunes de resistencia a la hipoxia y apoptosis serían de gran interés para posibles estudios futuros sobre tratamientos de MCL. La leucèmia és un tipus de càncer que comença en els teixits generadors de sang, com ara la medul·la òssia. Aquesta malaltia causa la producció d'un gran nombre de cèl·lules sanguínies anormals que van a parar al flux sanguini. Dins de la leucèmia trobem diferents tipus, sent el Limfoma de les cèl·lules del mantell (en endavant, Mantle Cell Lymphoma o MCL) el que pitjor pronòstic té, a causa de la curta mitjana de supervivència del pacient, propera als tres anys. Aquest tumor es caracteritza per la sobre-expressió de la ciclina D1, proteïna que ajuda a controlar la divisió cel·lular, i també per la unió d'aquesta proteïna a certes regions d'ADN involucrades en la regulació del procés de reparació del dany a l'ADN (en endavant, DNA-Damage Response o DDR). El present estudi té com a objectiu identificar les similituds entre l'expressió gènica derivada de la regulació per la ciclina D1 en Limfoma amb la que es dóna en el cas del dany en l'ADN. Aquest coneixement permetrà l'exploració dels mecanismes essencials de carcinogènesi i ajudarà en la identificació de gens que poden ser un objectiu terapèutic interessant en el procés de progressió tumoral. Addicionalment, es podrien trobar nous biomarcadors per al diagnòstic precoç de la malaltia. Amb l'addició de machine learning al procés d'anàlisi biològica, aquest projecte explora noves formes de millorar les metodologies tradicionals i impulsar la identificació de gens significativament enriquits que serviran als propòsits esmentats anteriorment. El resultat d'aquest procés analític és la precisa selecció de gens correlacionats amb la ciclina D1, involucrats en MCL i DDR, i la seva posterior anàlisi. Com a conclusió, els resultats obtinguts en aquest estudi van suggerir que el tractament del Notch pathway i el potencial estudi dels mecanismes comuns de resistència a la hipòxia i apoptosi serien de gran interès per a possibles estudis futurs sobre tractaments de MCL.

Journal of synchrotron radiation 26(2), 393 - 405 (2019). doi:10.1107/S1600577519001267, MXCuBE2 is the second-generation evolution of the MXCuBE beamline control software, initially developed and used at ESRF – the European Synchrotron. MXCuBE2 extends, in an intuitive graphical user interface (GUI), the functionalities and data collection methods available to users while keeping all previously available features and allowing for the straightforward incorporation of ongoing and future developments. MXCuBE2 introduces an extended abstraction layer that allows easy interfacing of any kind of macromolecular crystallography (MX) hardware component, whether this is a diffractometer, sample changer, detector or optical element. MXCuBE2 also works in strong synergy with the ISPyB Laboratory Information Management System, accessing the list of samples available for a particular experimental session and associating, either from instructions contained in ISPyB or from user input via the MXCuBE2 GUI, different data collection types to them. The development of MXCuBE2 forms the core of a fruitful collaboration which brings together several European synchrotrons and a software development factory and, as such, defines a new paradigm for the development of beamline control platforms for the European MX user community., Published by Wiley-Blackwell, [S.l.]

The web continues to grow as an application platform, with accessibility and platform independence as major benefits. It also makes it possible to tie services together in new ways through simple APIs. At MAX IV we are using web services for various purposes related to the control system, for example, monitoring servers and services, accessing alarm history, viewing control system status, managing system and users logs and running recurring jobs. Furthermore, all user management is also accessed via web applications, and even data analysis and experiment control can now be performed via web based interfaces. We make an effort to use existing tools whenever possible (e.g. Kibana, Prometheus), and otherwise develop systems in-house, based on current well established libraries and standards, such as JavaScript, Python, Apache, etc. This paper presents an overview of our activities in the field and describes different architectural decisions taken., Proceedings of the 16th Int. Conf. on Accelerator and Large Experimental Control Systems, ICALEPCS2017, Barcelona, Spain

The BioMAX beamline at MAX IV is devoted to macromolecular crystallography and will achieve a high level of experimental automation when its full potential is reached due to the usage of high end instrumentation and comprehensive software environment. The control system is based on Tango and Sardana for managing the main elements of the beamline. Data acquisition and experiment control is done through MXCuBE v3, which interfaces with the control layer. Currently, the most critical elements such as the detector and diffractometer are already integrated into the control system, whereas the integration of the sample changer has already started. BioMAX has received its first users, who successfully collected diffraction data and provided feedback on the general performance of the control system and its usability. The present work describes the main features of the control system and its operation, as well as the next instrument integration plans, Proceedings of the 16th Int. Conf. on Accelerator and Large Experimental Control Systems, ICALEPCS2017, Barcelona, Spain

Small currents need to be measured from a number of devices at a synchrotron and its beamlines. To meet this demand, MAX IV have joined a collaboration with ALBA to develop an electrometer that will ensure low current measurement capabilities and seamless integration into our Tango control system. The electrometers 4 independent channels can measure accurately in the fA range. Many devices produce larger currents and only need low sample rate. To make the electrometer more flexible, MAX IV have therefore developed a multiplexer with 8 independent channels. The multiplexer is both powered and controlled by the electrometer through its multipurpose IO interface. At most, an electrometer can control 4 multiplexers simultaneously giving a system with 32 channels, but the number of multiplexers can be chosen freely. The offset current introduced by the multiplexer is 45 pA and the noise is 3 pA. The offset is eliminated by settings in the electrometer. Current sweeps shows that currents steps as small as 10 pA can easily be measured and that switching time between channels before a steady signal is achieved is limited by the filter needed by the electrometer and not the multiplexer., Proceedings of the 16th Int. Conf. on Accelerator and Large Experimental Control Systems, ICALEPCS2017, Barcelona, Spain

Originally conceived at ESRF and first deployed in 2005 MXCuBE, Macromolecular Xtallography Customized Beamline Environment, has with its successor MXCuBE2, become a successful international collaboration. The aim of the collaboration is to develop a beamline control application for macromolecular crystallography (MX) that are independent of underlying instrument control software and thus deployable at the MX beamlines of any synchrotron source. The continued evolution of the functionality offered at MX beamlines is to a large extent facilitated by active software development. New demands and advances in technology have led to the development of a new version of MXCuBE, MXCuBE3, The design of which was inspired by the results of a technical pre-study and user survey. MXCuBE3 takes advantage of the recent development in web technologies such as React and Redux to create an intuitive and user friendly application. The access to the application from any web browser further simplifies the operation and natively facilitates the execution of remote experiments., Proceedings of the 16th Int. Conf. on Accelerator and Large Experimental Control Systems, ICALEPCS2017, Barcelona, Spain

Preprint The reaction of the low sterically hindered heteroscorpionate lithium acetamidinates [Li(κ3-NNN)(thf)] {NNN = pbpamd (1) [pbpamd = N,N′-diisopropylbis(3,5-dimethylpyrazol-1-yl)acetamidinate], tbpamd (2) [tbpamd = N-ethyl-N′-tert-butylbis(3,5-dimethylpyrazol-1-yl)acetamidinate], ttbpamd (3) [ttbpamd = N,N′-di-tert-butylbis(3,5-dimethylpyrazol-1-yl)acetamidinate], phbpamd (4) [phbpamd = N,N′-di-p-tolylbis(3,5-dimethylpyrazol-1-yl)acetamidinate] and the highly sterically demanding [Li(κ3-phbptamd)(thf)] (5) [phbptamd = N,N′-di-p-tolylbis(3,5-di-tert-butylpyrazol-1-yl)acetamidinate] with the commercially available Grignard reagent tBuMgCl in an equimolecular ratio yielded the magnesium tert-butyl heteroscorpionates [Mg(tBu)(κ3-NNN)] [NNN = pbpamd (6), tbpamd (7), ttbpamd (8), and phbptamd (9)]. In addition, subsequent reaction of monoalkyls 6–8 with two additional equivalents of tBuMgCl gave rise to two different classes of chiral tetraalkyls, which contain apical methine C–H activated heteroscorpionates that show two possible coordination modes, namely, the tetranuclear complexes [{(tBu)Mg(κ3-N,N,N;κ2-C,N)Mg(tBu)}2{μ-O,O-(OC4H8O)}] (κ3-N,N,N;κ2-C,N = pbpamd–10, tbpamd–11a) and [(tBu)Mg(κ2-N,N;κ2-N,N)Mg(tBu){μ-O,O-(OC4H8O)}]2 (κ2-N,N;κ2-N,N = tbpamd–11b). This reaction for 8 was unsuccessful, but an analog such as dinuclear complex [(thf)(tBu)Mg(κ2-N,N;κ2-N,N)Mg(tBu)(thf)] (κ2-N,N;κ2-N,N = phbpamd–12) could be obtained from its lithium salt. Contrary to complexes 10–12, the C–H activation process was not observed for complex 9, but interestingly, the coordination of one additional equivalent of MgtBu2 afforded dinuclear complex [Mg(tBu)(κ3-phbptamd){Mg(tBu)2}] (13). Similarly, coordination of MgtBu2 to 10 produces chiral trinuclear [{(tBu)Mg(pbpamd–)Mg(tBu)}{μ-O,O-(OC4H8O)}{Mg(tBu)2(thf)}] (14). The X-ray crystal structures of complexes 4, 6, 8, 9, 11b, 12, 13, and 14 confirm the nuclearity of each family, and the existence of apical σ-C(sp3)–Mg (14) and extended π-C2N2(sp2)–Mg2 (11b and 12) covalent bonds have unambiguously been also confirmed. Furthermore, mononuclear compounds 8 and 9, tetranuclear compound 10, and dinuclear compounds 12 and 13 can act as highly efficient single-component living initiators for the ring-opening polymerization of rac-lactide. More interestingly, the most sterically hindered initiators exhibit enhanced levels of heteroselectivity on the PLAs, with 9 reaching Ps values up to 0.85.