Sensing and Visualizing Social Context from Spatial Proximity

The concept of pervasive computing, as introduced by Marc Weiser under the name ubiquitous computing in the early 90s, spurred research into various kinds of context-aware systems and applications. There is a wide range of contextual parameters, including location, time, temperature, devices and people in proximity, which have been part of the initial ideas about context-aware computing. While locational context is already a well understood concept, social context---based on the people around us---proves to be harder to grasp and to operationalize. This work continues the line of research into social context, which is based on the proximity and meeting patterns of people in the physical space. It takes this research out of the lab and out of well controlled situations into our urban environments, which are full of ambiguity and opportunities. The key to this research is the tool that caused dramatic change in individual and collective behavior during the last 20 years and which is a manifestation of many of the ideas of the pervasive computing paradigm: the mobile phone. In this work, the mobile is regarded as a proxy for people. Through it, the social environment becomes accessible to digital measurement and processing. To understand the large amount of data that now becomes available to automatic measurement, we will turn to the discipline of social network analysis. It provides powerful methods, that are able to condense data and extract relevant meaning. Visualization helps to understand and interpret the results. This thesis contains a number of experiments, that demonstrate how the automatic measurement of social proximity data through Bluetooth can be used to measure variables of personal behavior, group behavior and the behavior of groups in relation to places. The principal contributions are: * A methodology to visualize personal social context by using an ego proximity network. Specific episodes can be localized and compared. * method to compare different days in terms of social context, e.g. to support automatic diary applications. * A method to compose social geographic maps. Locations of similar social context are detected and combined. * Functions to measure short-term changes in social activity, based on the distinction between strange and familiar devices. * The characterization of Bluetooth inquiries for social proximity sensing. * A dataset of Bluetooth sightings from an ego perspective in seven different settings. Additionally, some settings feature multiple stationary scanners and Cell-ID measurements. * Soft- and hardware to capture, collect, store and analyze Bluetooth proximity data

CollaborationBus: An Editor for the Easy Configuration of Complex Ubiquitous Environment

Early sensor-based infrastructures were often developed by experts with a thorough knowledge of base technology for sensing information, for processing the captured data, and for adapting the system’s behaviour accordingly. In this paper we argue that also end-users should be able to configure Ubiquitous Computing environments. We introduce the CollaborationBus application: a graphical editor that provides abstractions from base technology and thereby allows multifarious users to configure Ubiquitous Computing environments. By composing pipelines users can easily specify the information flows from selected sensors via optional filters for processing the sensor data to actuators changing the system behaviour according to the users’ wishes. Users can compose pipelines for both home and work environments. An integrated sharing mechanism allows them to share their own compositions, and to reuse and build upon others’ compositions. Real-time visualisations help them understand how the information flows through their pipelines. In this paper we present the concept, implementation, and early user feedback of the CollaborationBus application

FMI for Co-Simulation of Embedded Control Software

Increased complexity of cyber-physical systems within the maritime industry demands closer cooperation be-tween engineering disciplines. The functional mockup interface (FMI) is an initiative aiding cross-discipline in-teraction by providing, a widely accepted, standard for model exchange and co-simulation. The standard is sup-ported by a number of modelling tools. However, to im-plement it on an existing platform requires adaptation. This paper investigates how to adapt the software of an embedded control system to comply with the FMI for co-simulation standard. In particular, we suggest a way of advancing the clock of a real time operating system (RTOS), by overwriting the idle thread and waiting for a signal to start execution until return to idle. This ap-proach ensures a deterministic and temporal execution of the simulation across multiple nodes. As proof of concept, a co-simulation is conducted, showing that the control system of an SCR (selective catalyst reduction) emission reduction system can be packed in a functional mockup unit (FMU) and co-simulated with a physical model, built in Ptolemy II. Results show that FMI can be used for co-simulation of an embedded SCR control soft-ware and for control software development

CollaborationBus: An Editor for the Easy Configuration of Complex Ubiquitous Environment

Early sensor-based infrastructures were often developed by experts with a thorough knowledge of base technology for sensing information, for processing the captured data, and for adapting the system’s behaviour accordingly. In this paper we argue that also end-users should be able to configure Ubiquitous Computing environments. We introduce the CollaborationBus application: a graphical editor that provides abstractions from base technology and thereby allows multifarious users to configure Ubiquitous Computing environments. By composing pipelines users can easily specify the information flows from selected sensors via optional filters for processing the sensor data to actuators changing the system behaviour according to the users’ wishes. Users can compose pipelines for both home and work environments. An integrated sharing mechanism allows them to share their own compositions, and to reuse and build upon others’ compositions. Real-time visualisations help them understand how the information flows through their pipelines. In this paper we present the concept, implementation, and early user feedback of the CollaborationBus application

Intrinsic anti-Stokes emission in living HeLa cells

Intrinsic fluorescence of biological material, also called auto-fluorescence, is a well-known phenomenon and has in recent years been used for imaging, diagnostics and cell viability studies. Here we show that in addition to commonly observed auto-fluorescence, intrinsic anti-Stokes emission can also be observed under 560 nm or 633 nm excitation. The anti-Stokes emission is shown to be spatially located on/in the mitochondria. The findings presented here show that sensitive imaging experiments e.g. single molecule experiments or two-photon excitation imaging can be compromised if intracellular anti-Stokes emission is not accounted for. On the other hand, we suggest that this anti-Stokes emission could be exploited as an additional modality for mitochondria visualization and cell viability investigation even in systems that are already labeled with commonly used fluorophores that rely on normal Stokes-based detection

A Chemistry of Organization: Combinatory Structural Analysis and Design

This paper is a response to the call for models of organization design as a science revealing the inner composition of organization and specifying the laws to be respected when crafting it. It maintains that the needed science is a chemistry of organization, addressing the combination of 'organizational elements' playing a role analogous to that of chemical elements in composing a variety of substances. Drawing both on classic organization design theory and on configurational and complementarity-based approaches, the paper specifies a set of basic organizational elements and a set of combinatory laws regulating their effective combinations. Testable propositions are derived on the necessary and sufficient conditions that the composition of organizations should have respect for achieving high levels of efficiency and innovation. These propositions are tested empirically on a sample of firms, using an innovative application of Boolean algebra

Synthesis, oligonucleotide incorporation and fluorescence properties in DNA of a bicyclic thymine analogue

Fluorescent base analogues (FBAs) have emerged as a powerful class of molecular reporters of location and environment for nucleic acids. In our overall mission to develop bright and useful FBAs for all natural nucleobases, herein we describe the synthesis and thorough characterization of bicyclic thymidine (bT), both as a monomer and when incorporated into DNA. We have developed a robust synthetic route for the preparation of the bT DNA monomer and the corresponding protected phosphoramidite for solid-phase DNA synthesis. The bT deoxyribonucleoside has a brightness value of 790 M−1cm−1in water, which is comparable or higher than most fluorescent thymine analogues reported. When incorporated into DNA, bT pairs selectively with adenine without perturbing the B-form structure, keeping the melting thermodynamics of the B-form duplex DNA virtually unchanged. As for most fluorescent base analogues, the emission of bT is reduced inside DNA (4.5- and 13-fold in single- and double-stranded DNA, respectively). Overall, these properties make bT an interesting thymine analogue for studying DNA and an excellent starting point for the development of brighter bT derivatives

A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer

Funding Information: D.B. has consulted for NanoString, reports honoraria from AstraZeneca and has a patent (PCT/GB2020/050221) issued on methods for cancer prognostication. J.R. and M.A.B. have consulted for Achilles Therapeutics. N.M. has stock options in and has consulted for Achilles Therapeutics. N.M. holds European patents relating to targeting neoantigens (PCT/EP2016/059401), identifying patient response to immune checkpoint blockade (PCT/EP2016/071471), determining HLA loss of heterozygosity (PCT/GB2018/052004) and predicting survival rates of patients with cancer (PCT/GB2020/050221). A.H. attended one advisory board for Abbvie, Roche and GRAIL, and reports personal fees from Abbvie, Boehringer Ingelheim, Takeda, AstraZeneca, Daiichi Sankyo, Merck Serono, Merck/MSD, UCB and Roche for delivering general education/training in clinical trials. A.H. owned shares in Illumina and Thermo Fisher Scientific (sold in 2020) and receives fees for membership of Independent Data Monitoring Committees for Roche-sponsored clinical trials. S.A.Q. is co-founder and Chief Scientific Officer of Achilles Therapeutics. A.C.H. is a board member and equity holder in ImmunoQure, AG and Gamma Delta Therapeutics, and is an equity holder in Adaptate Biotherapeutics and chair of the scientific advisory board. C.S. acknowledges grant support from Pfizer, AstraZeneca, Bristol Myers Squibb, Roche-Ventana, Boehringer Ingelheim, Archer Dx Inc (collaboration in minimal residual disease-sequencing technologies) and Ono Pharmaceuticals, is an AstraZeneca Advisory Board member and Chief Investigator for the MeRmaiD1 clinical trial. C.S has consulted for Amgen, AstraZeneca, Bicycle Therapeutics, Bristol Myers Squibb, Celgene, Genentech, GlaxoSmithKline, GRAIL, Illumina, Medixci, Metabomed, MSD, Novartis, Pfizer, Roche-Ventana and Sarah Cannon Research Institute. C.S. has stock options in Apogen Biotechnologies, Epic Biosciences and GRAIL, and has stock options and is co-founder of Achilles Therapeutics. C.S. holds patents relating: to assay technology to detect tumor recurrence (PCT/GB2017/053289); to targeting neoantigens (PCT/EP2016/059401), identifying patent response to immune checkpoint blockade (PCT/EP2016/071471), determining HLA loss of heterozygosity (PCT/GB2018/052004), predicting survival rates of patients with cancer (PCT/GB2020/050221); to treating cancer by targeting Insertion/deletion (indel) mutations (PCT/GB2018/051893); to identifying indel mutation targets (PCT/GB2018/051892); to methods for lung cancer detection (PCT/US2017/028013); and to identifying responders to cancer treatment (PCT/GB2018/051912). The remaining authors declare no competing interests. Funding Information: We thank the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (funded by Wellcome Trust grant no. 203141/Z/16/Z) for the generation and initial processing of the RNA-seq data from sorted TILs. We thank S. Bola for technical support and S. Vanloo for administrative support. The GTEx project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by the NCI, NHGRI, NHLBI, NIDA, NIMH and NINDS. Y.W. was supported by a Wellcome Trust Clinical Research Career Development Fellowship (no. 220589/Z/20/Z), an Academy of Medical Sciences Starter Grant for Clinical Lecturers, a National Institute for Health Research (NIHR) Academic Clinical Lectureship and the NIHR University College London Hospitals Biomedical Research Centre. D.B. was supported by funding from the NIHR University College London Hospitals Biomedical Research Centre, the ideas 2 innovation translation scheme at the Francis Crick Institute, the Breast Cancer Research Foundation (BCRF) and a Cancer Research UK (CRUK) Early Detection and Diagnosis Project award. M.J.H. is a CRUK Fellow and has received funding from CRUK, NIHR, Rosetrees Trust, UKI NETs and the NIHR University College London Hospitals Biomedical Research Centre. C.S. is Royal Society Napier Research Professor. This work was supported by the Francis Crick Institute which receives its core funding from CRUK (no. FC001169), the UK Medical Research Council (no. FC001169) and the Wellcome Trust (no. FC001169). This research was funded in whole, or in part, by the Wellcome Trust (no. FC001169). For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. C.S. is funded by CRUK (TRACERx, PEACE and CRUK Cancer Immunotherapy Catalyst Network), CRUK Lung Cancer Centre of Excellence (no. C11496/A30025), the Rosetrees Trust, Butterfield and Stoneygate Trusts, NovoNordisk Foundation (ID16584), Royal Society Professorship Enhancement Award (no. RP/EA/180007), the NIHR Biomedical Research Centre at University College London Hospitals, the CRUK–University College London Centre, Experimental Cancer Medicine Centre and the BCRF. This work was supported by a Stand Up To Cancer‐LUNGevity-American Lung Association Lung Cancer Interception Dream Team Translational Research Grant (grant no. SU2C-AACR-DT23-17 to S. M. Dubinett and A. E. Spira). Stand Up To Cancer is a division of the Entertainment Industry Foundation. Research grants are administered by the American Association for Cancer Research, the Scientific Partner of SU2C. C.S. receives funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (no. FP7/2007-2013) Consolidator Grant (no. FP7-THESEUS-617844), European Commission ITN (no. FP7-PloidyNet 607722), an ERC Advanced Grant (PROTEUS) from the ERC under the European Union’s Horizon 2020 research and innovation program (grant no. 835297), and Chromavision from the European Union’s Horizon 2020 research and innovation program (grant no. 665233). Publisher Copyright: © 2022, The Author(s).Peer reviewedPublisher PD