STAMINA: Bioinformatics Platform for Monitoring and Mitigating Pandemic Outbreaks

This paper presents the components and integrated outcome of a system that aims to achieve early detection, monitoring and mitigation of pandemic outbreaks. The architecture of the platform aims at providing a number of pandemic-response-related services, on a modular basis, that allows for the easy customization of the platform to address user’s needs per case. This customization is achieved through its ability to deploy only the necessary, loosely coupled services and tools for each case, and by providing a common authentication, data storage and data exchange infrastructure. This way, the platform can provide the necessary services without the burden of additional services that are not of use in the current deployment (e.g., predictive models for pathogens that are not endemic to the deployment area). All the decisions taken for the communication and integration of the tools that compose the platform adhere to this basic principle. The tools presented here as well as their integration is part of the project STAMINA

CLARITY Screening Service for Climate Hazards, Impacts and Effects of the Adaptation Options

The CLARITY project (www.clarity-h2020.eu) aims to implement a new generation of climate services that allow the service users to perform an initial assessment of the expected climate change effects in the project area, as well as an initial assessment of the need for and of the usability of the adaptation options in the early project planning phase. The target users of this service are the consultants and urban planning experts that aren’t climate change experts but need to produce standardized reports indicating the climate hazard, exposure and impact data, as well as the expected impact of the adaptation options in the project area, as a part of the project planning. The initial implementation of this service uses the available open data to calculate the local heat hazard, population exposure and related impact indicators at the project location on the fly. In the initial implementation, the heat related can be automatically calculated for more than 400 European cities, with a spatial resolution of 500 × 500 m2. Extension to the flooding hazards and related impacts is in implementation. This article will describe in more detail the workflow and the technical implementation of the CLARITY screening service and discuss the value, potential and the limitations of the current service implementation

Asymmetric Choreography in Pairs of Orthogonal Rotors

An asymmetric mechanism for correlated motion occurring in noninteracting pairs of adjacent orthogonal 1,4-bis(carboxyethynyl)bicyclo[1.1.1]pentane (BCP) rotators 1 in the solid state is unraveled and shown to play an important role in understanding the dynamics in the crystalline rotor, Bu4N+[1–]·H2O. Single crystal X-ray diffraction and calculation of rotor–rotor interaction energies combined with variable-temperature, variable-field 1H spin–lattice relaxation experiments led to the identification and microscopic rationalization of two distinct relaxation processes.Work in Bellaterra and Tarragona was supported by the Spanish Ministerio de Economía y Competitividad (projects FIS2015-64886-C5-4-P and CTQ2017-87269-P) and Generalitat de Catalunya (2014GR301 and 2014GR199). E.C. acknowledges the support of the Spanish MINECO through the Severo Ochoa Centers of Excellence Program under grant SEV-2015-0496. J.K. and J.M. gratefully acknowledge financial support from the European Research Council under the European Community’s Framework Programme (FP7/2007-2013) ERC grant agreement no. 227756 and the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic (RVO: 61388963). This material is based upon work supported by the National Science Foundation under grant no. CHE-1566435. Work at Orsay was supported by the CNRS. Work at Angers was supported by the CNRS and the Région des Pays de la Loire grant MOVAMOL. Joint work at Angers, Orsay, and Prague was supported by the Ministère de l’Europe et des Affaires Etrangères under the grant PHC Barrande no. 864563J.Peer reviewe

Crystalline Arrays of Pairs of Molecular Rotors: Correlated Motion, Rotational Barriers, and Space-Inversion Symmetry Breaking Due to Conformational Mutations

The rod-like molecule bis­((4-(4-pyridyl)­ethynyl)­bicyclo[2.2.2]­oct-1-yl)­buta-1,3-diyne, <b>1</b>, contains two 1,4-bis­(ethynyl)­bicyclo[2.2.2]­octane (BCO) chiral rotators linked by a diyne fragment and self-assembles in a one-dimensional, monoclinic <i>C</i>2/<i>c</i> centrosymmetric structure where two equilibrium positions with large occupancy imbalance (88% versus 12%) are identified on a single rotor site. Combining variable-temperature (70–300 K) proton spin–lattice relaxation, ¹H <i>T</i>₁^–1, at two different ¹H Larmor frequencies (55 and 210 MHz) and DFT calculations of rotational barriers, we were able to assign two types of Brownian rotators with different activation energies, 1.85 and 6.1 kcal mol^–1, to the two ¹H spin–lattice relaxation processes on the single rotor site. On the basis of DFT calculations, the low-energy process has been assigned to adjacent rotors in a well-correlated synchronous motion, whereas the high-energy process is the manifestation of an abrupt change in their kinematics once two blades of adjacent rotors are seen to rub together. Although crystals of <b>1</b> should be second harmonic inactive, a large second-order optical response is recorded when the electric field oscillates in a direction parallel to the unique rotor axle director. We conclude that conformational mutations by torsional interconversion of the three blades of the BCO units break space-inversion symmetry in sequences of mutamers in dynamic equilibrium in the crystal in domains at a mesoscopic scale comparable with the wavelength of light used. A control experiment was performed with a crystalline film of a similar tetrayne molecule, 1,4-bis­(3-((trimethylsilyl)­ethynyl)­bicyclo­[1.1.1]­pent-1-yl)­buta-1,3-diyne, whose bicyclopentane units can rotate but are achiral and produce no second-order optical response

Crystalline Arrays of Pairs of Molecular Rotors: Correlated Motion, Rotational Barriers, and Space-Inversion Symmetry Breaking Due to Conformational Mutations

The rod-like molecule bis­((4-(4-pyridyl)­ethynyl)­bicyclo[2.2.2]­oct-1-yl)­buta-1,3-diyne, <b>1</b>, contains two 1,4-bis­(ethynyl)­bicyclo[2.2.2]­octane (BCO) chiral rotators linked by a diyne fragment and self-assembles in a one-dimensional, monoclinic <i>C</i>2/<i>c</i> centrosymmetric structure where two equilibrium positions with large occupancy imbalance (88% versus 12%) are identified on a single rotor site. Combining variable-temperature (70–300 K) proton spin–lattice relaxation, ¹H <i>T</i>₁^–1, at two different ¹H Larmor frequencies (55 and 210 MHz) and DFT calculations of rotational barriers, we were able to assign two types of Brownian rotators with different activation energies, 1.85 and 6.1 kcal mol^–1, to the two ¹H spin–lattice relaxation processes on the single rotor site. On the basis of DFT calculations, the low-energy process has been assigned to adjacent rotors in a well-correlated synchronous motion, whereas the high-energy process is the manifestation of an abrupt change in their kinematics once two blades of adjacent rotors are seen to rub together. Although crystals of <b>1</b> should be second harmonic inactive, a large second-order optical response is recorded when the electric field oscillates in a direction parallel to the unique rotor axle director. We conclude that conformational mutations by torsional interconversion of the three blades of the BCO units break space-inversion symmetry in sequences of mutamers in dynamic equilibrium in the crystal in domains at a mesoscopic scale comparable with the wavelength of light used. A control experiment was performed with a crystalline film of a similar tetrayne molecule, 1,4-bis­(3-((trimethylsilyl)­ethynyl)­bicyclo­[1.1.1]­pent-1-yl)­buta-1,3-diyne, whose bicyclopentane units can rotate but are achiral and produce no second-order optical response

Crystalline Arrays of Pairs of Molecular Rotors: Correlated Motion, Rotational Barriers, and Space-Inversion Symmetry Breaking Due to Conformational Mutations

The rod-like molecule bis­((4-(4-pyridyl)­ethynyl)­bicyclo[2.2.2]­oct-1-yl)­buta-1,3-diyne, <b>1</b>, contains two 1,4-bis­(ethynyl)­bicyclo[2.2.2]­octane (BCO) chiral rotators linked by a diyne fragment and self-assembles in a one-dimensional, monoclinic <i>C</i>2/<i>c</i> centrosymmetric structure where two equilibrium positions with large occupancy imbalance (88% versus 12%) are identified on a single rotor site. Combining variable-temperature (70–300 K) proton spin–lattice relaxation, ¹H <i>T</i>₁^–1, at two different ¹H Larmor frequencies (55 and 210 MHz) and DFT calculations of rotational barriers, we were able to assign two types of Brownian rotators with different activation energies, 1.85 and 6.1 kcal mol^–1, to the two ¹H spin–lattice relaxation processes on the single rotor site. On the basis of DFT calculations, the low-energy process has been assigned to adjacent rotors in a well-correlated synchronous motion, whereas the high-energy process is the manifestation of an abrupt change in their kinematics once two blades of adjacent rotors are seen to rub together. Although crystals of <b>1</b> should be second harmonic inactive, a large second-order optical response is recorded when the electric field oscillates in a direction parallel to the unique rotor axle director. We conclude that conformational mutations by torsional interconversion of the three blades of the BCO units break space-inversion symmetry in sequences of mutamers in dynamic equilibrium in the crystal in domains at a mesoscopic scale comparable with the wavelength of light used. A control experiment was performed with a crystalline film of a similar tetrayne molecule, 1,4-bis­(3-((trimethylsilyl)­ethynyl)­bicyclo­[1.1.1]­pent-1-yl)­buta-1,3-diyne, whose bicyclopentane units can rotate but are achiral and produce no second-order optical response

STAMINA: Bioinformatics Platform for Monitoring and Mitigating Pandemic Outbreaks

This paper presents the components and integrated outcome of a system that aims to achieve early detection, monitoring and mitigation of pandemic outbreaks. The architecture of the platform aims at providing a number of pandemic-response-related services, on a modular basis, that allows for the easy customization of the platform to address user&rsquo;s needs per case. This customization is achieved through its ability to deploy only the necessary, loosely coupled services and tools for each case, and by providing a common authentication, data storage and data exchange infrastructure. This way, the platform can provide the necessary services without the burden of additional services that are not of use in the current deployment (e.g., predictive models for pathogens that are not endemic to the deployment area). All the decisions taken for the communication and integration of the tools that compose the platform adhere to this basic principle. The tools presented here as well as their integration is part of the project STAMINA