Making SPIFFI SPIFFIER: Upgrade of the SPIFFI instrument for use in ERIS and performance analysis from re-commissioning

SPIFFI is an AO-fed integral field spectrograph operating as part of SINFONI on the VLT, which will be upgraded and reused as SPIFFIER in the new VLT instrument ERIS. In January 2016, we used new technology developments to perform an early upgrade to optical subsystems in the SPIFFI instrument so ongoing scientific programs can make use of enhanced performance before ERIS arrives in 2020. We report on the upgraded components and the performance of SPIFFI after the upgrade, including gains in throughput and spatial and spectral resolution. We show results from re-commissioning, highlighting the potential for scientific programs to use the capabilities of the upgraded SPIFFI. Finally, we discuss the additional upgrades for SPIFFIER which will be implemented before it is integrated into ERIS.Comment: 20 pages, 12 figures. Proceedings from SPIE Astronomical Telescopes and Instrumentation 201

Hybrid-learning for social design

Underlying causes of conflict, inequity, and injustice remain deeply entrenched in the lives of people ranging from impoverished villages to overpopulated megalopolises. To help address these complex issues, social design brings together designers from varying disciplines to address the needs of the community. While universities across the world recognize the need to introduce social design pedagogy into their curriculum, many programs remain confined within Western post-graduate education. In response, two multidisciplinary professors initiated a team-taught \u27Design for Social Change\u27 course in an undergraduate design program in Dubai, UAE. Open to students across disciplines, the course followed a hybrid-learning approach to planning, conducting, and evaluating learning activities. The methodology empowered students to determine their project interest, cooperatively build research, and value their diverse skills. This paper introduces the notion of hybrid-learning, collabor-active team-teaching in an interdisciplinary classroom, and applies the methodology to a social design course in the MENA region. This paper has been presented as part of the Tasmeem Exploration Platform during Tasmeem Conference, Doha, 2013

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

Markov (state) models (MSMs) and related models of molecular kinetics have recently received a surge of interest as they can systematically reconcile simulation data from either a few long or many short simulations and allow us to analyze the essential metastable structures, thermodynamics, and kinetics of the molecular system under investigation. However, the estimation, validation, and analysis of such models is far from trivial and involves sophisticated and often numerically sensitive methods. In this work we present the opensource Python package PyEMMA (http://pyemma.org) that provides accurate and efficient algorithms for kinetic model construction. PyEMMA can read all common molecular dynamics data formats, helps in the selection of input features, provides easy access to dimension reduction algorithms such as principal component analysis (PCA) and time-lagged independent component analysis (TICA) and clustering algorithms such as k-means, and contains estimators for MSMs, hidden Markov models, and several other models. Systematic model validation and error calculation methods are provided. PyEMMA offers a wealth of analysis functions such that the user can conveniently compute molecular observables of interest. We have derived a systematic and accurate way to coarse-grain MSMs to few states and to illustrate the structures of the metastable states of the system. Plotting functions to produce a manuscript-ready presentation of the results are available. In this work, we demonstrate the features of the software and show new methodological concepts and results produced by PyEMMA

Framework, principles and recommendations for utilising participatory methodologies in the co-creation and evaluation of public health interventions

Background: Due to the chronic disease burden on society, there is a need for preventive public health interventions to stimulate society towards a healthier lifestyle. To deal with the complex variability between individual lifestyles and settings, collaborating with end-users to develop interventions tailored to their unique circumstances has been suggested as a potential way to improve effectiveness and adherence. Co-creation of public health interventions using participatory methodologies has shown promise but lacks a framework to make this process systematic. The aim of this paper was to identify and set key principles and recommendations for systematically applying participatory methodologies to co-create and evaluate public health interventions. Methods: These principles and recommendations were derived using an iterative reflection process, combining key learning from published literature in addition to critical reflection on three case studies conducted by research groups in three European institutions, all of whom have expertise in co-creating public health interventions using different participatory methodologies. Results: Key principles and recommendations for using participatory methodologies in public health intervention co-creation are presented for the stages of: Planning (framing the aim of the study and identifying the appropriate sampling strategy); Conducting (defining the procedure, in addition to manifesting ownership); Evaluating (the process and the effectiveness) and Reporting (providing guidelines to report the findings). Three scaling models are proposed to demonstrate how to scale locally developed interventions to a population level. Conclusions: These recommendations aim to facilitate public health intervention co-creation and evaluation utilising participatory methodologies by ensuring the process is systematic and reproducible

Scalable transactions in the cloud: partitioning revisited

Lecture Notes in Computer Science, 6427Cloud computing is becoming one of the most used paradigms to deploy highly available and scalable systems. These systems usually demand the management of huge amounts of data, which cannot be solved with traditional nor replicated database systems as we know them. Recent solutions store data in special key-value structures, in an approach that commonly lacks the consistency provided by transactional guarantees, as it is traded for high scalability and availability. In order to ensure consistent access to the information, the use of transactions is required. However, it is well-known that traditional replication protocols do not scale well for a cloud environment. Here we take a look at current proposals to deploy transactional systems in the cloud and we propose a new system aiming at being a step forward in achieving this goal. We proceed to focus on data partitioning and describe the key role it plays in achieving high scalability.This work has been partially supported by the Spanish Government under grant TIN2009-14460-C03-02 and by the Spanish MEC under grant BES-2007-17362 and by project ReD Resilient Database Clusters (PDTC/EIA-EIA/109044/2008)

Scalar and vector Slepian functions, spherical signal estimation and spectral analysis

It is a well-known fact that mathematical functions that are timelimited (or spacelimited) cannot be simultaneously bandlimited (in frequency). Yet the finite precision of measurement and computation unavoidably bandlimits our observation and modeling scientific data, and we often only have access to, or are only interested in, a study area that is temporally or spatially bounded. In the geosciences we may be interested in spectrally modeling a time series defined only on a certain interval, or we may want to characterize a specific geographical area observed using an effectively bandlimited measurement device. It is clear that analyzing and representing scientific data of this kind will be facilitated if a basis of functions can be found that are "spatiospectrally" concentrated, i.e. "localized" in both domains at the same time. Here, we give a theoretical overview of one particular approach to this "concentration" problem, as originally proposed for time series by Slepian and coworkers, in the 1960s. We show how this framework leads to practical algorithms and statistically performant methods for the analysis of signals and their power spectra in one and two dimensions, and, particularly for applications in the geosciences, for scalar and vectorial signals defined on the surface of a unit sphere.Comment: Submitted to the 2nd Edition of the Handbook of Geomathematics, edited by Willi Freeden, Zuhair M. Nashed and Thomas Sonar, and to be published by Springer Verlag. This is a slightly modified but expanded version of the paper arxiv:0909.5368 that appeared in the 1st Edition of the Handbook, when it was called: Slepian functions and their use in signal estimation and spectral analysi

Phosphorylation of SOS1 on tyrosine 1196 promotes its RAC GEF activity and contributes to BCR-ABL leukemogenesis

Son of Sevenless 1 (SOS1) is a dual guanine nucleotide exchange factor (GEF) that activates the small GTPases RAC and RAS. Although the molecular mechanisms of RAS GEF catalysis have been unveiled, how SOS1 acquires RAC GEF activity and what is the physio-pathological relevance of this activity is much less understood. Here we show that SOS1 is tyrosine phosphorylated on Y1196 by ABL. Phosphorylation of Y1196 controls SOS1 inter-molecular interaction, is required to promote the exchange of nucleotides on RAC in vitro and for platelet-derived growth factor (PDGF) activation of RAC- and RAC-dependent actin remodeling and cell migration. SOS1 is also phosphorylated on Y1196 by BCR-ABL in chronic myelogenous leukemic cells. Importantly, in these cells, SOS1 is required for BCR-ABL-mediated activation of RAC, cell proliferation and transformation in vitro and in a xenograft mouse model. Finally, genetic removal of Sos1 in the bone marrow-derived cells (BMDCs) from Sos1fl/flmice and infected with BCR-ABL causes a significant delay in the onset of leukemogenesis once BMDCs are injected into recipient, lethally irradiated mice. Thus, SOS1 is required for full transformation and critically contribute to the leukemogenic potential of BCR-ABL