| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Fallows, Richard A., et al.
(author)
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A LOFAR observation of ionospheric scintillation from two simultaneous travelling ionospheric disturbances
- 2020
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In: Journal of Space Weather and Space Climate. - : EDP Sciences. - 2115-7251. ; 10
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Journal article (peer-reviewed)abstract
- This paper presents the results from one of the first observations of ionospheric scintillation taken using the Low-Frequency Array (LOFAR). The observation was of the strong natural radio source Cassiopeia A, taken overnight on 18-19 August 2013, and exhibited moderately strong scattering effects in dynamic spectra of intensity received across an observing bandwidth of 10-80 MHz. Delay-Doppler spectra (the 2-D FFT of the dynamic spectrum) from the first hour of observation showed two discrete parabolic arcs, one with a steep curvature and the other shallow, which can be used to provide estimates of the distance to, and velocity of, the scattering plasma. A cross-correlation analysis of data received by the dense array of stations in the LOFAR "core" reveals two different velocities in the scintillation pattern: a primary velocity of similar to 20-40 ms(-1) with a north-west to south-east direction, associated with the steep parabolic arc and a scattering altitude in the F-region or higher, and a secondary velocity of similar to 110 ms(-1) with a north-east to south-west direction, associated with the shallow arc and a scattering altitude in the D-region. Geomagnetic activity was low in the mid-latitudes at the time, but a weak sub-storm at high latitudes reached its peak at the start of the observation. An analysis of Global Navigation Satellite Systems (GNSS) and ionosonde data from the time reveals a larger-scale travelling ionospheric disturbance (TID), possibly the result of the high-latitude activity, travelling in the north-west to south-east direction, and, simultaneously, a smaller-scale TID travelling in a north-east to south-west direction, which could be associated with atmospheric gravity wave activity. The LOFAR observation shows scattering from both TIDs, at different altitudes and propagating in different directions. To the best of our knowledge this is the first time that such a phenomenon has been reported.
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| 3. |
- Forouzanfar, Mohammad H, et al.
(author)
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Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks in 188 countries, 1990-2013 : a systematic analysis for the Global Burden of Disease Study 2013.
- 2015
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In: The Lancet. - 0140-6736 .- 1474-547X. ; 386:10010, s. 2287-2323
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Journal article (peer-reviewed)abstract
- BACKGROUND: The Global Burden of Disease, Injuries, and Risk Factor study 2013 (GBD 2013) is the first of a series of annual updates of the GBD. Risk factor quantification, particularly of modifiable risk factors, can help to identify emerging threats to population health and opportunities for prevention. The GBD 2013 provides a timely opportunity to update the comparative risk assessment with new data for exposure, relative risks, and evidence on the appropriate counterfactual risk distribution.METHODS: Attributable deaths, years of life lost, years lived with disability, and disability-adjusted life-years (DALYs) have been estimated for 79 risks or clusters of risks using the GBD 2010 methods. Risk-outcome pairs meeting explicit evidence criteria were assessed for 188 countries for the period 1990-2013 by age and sex using three inputs: risk exposure, relative risks, and the theoretical minimum risk exposure level (TMREL). Risks are organised into a hierarchy with blocks of behavioural, environmental and occupational, and metabolic risks at the first level of the hierarchy. The next level in the hierarchy includes nine clusters of related risks and two individual risks, with more detail provided at levels 3 and 4 of the hierarchy. Compared with GBD 2010, six new risk factors have been added: handwashing practices, occupational exposure to trichloroethylene, childhood wasting, childhood stunting, unsafe sex, and low glomerular filtration rate. For most risks, data for exposure were synthesised with a Bayesian meta-regression method, DisMod-MR 2.0, or spatial-temporal Gaussian process regression. Relative risks were based on meta-regressions of published cohort and intervention studies. Attributable burden for clusters of risks and all risks combined took into account evidence on the mediation of some risks such as high body-mass index (BMI) through other risks such as high systolic blood pressure and high cholesterol.FINDINGS: All risks combined account for 57·2% (95% uncertainty interval [UI] 55·8-58·5) of deaths and 41·6% (40·1-43·0) of DALYs. Risks quantified account for 87·9% (86·5-89·3) of cardiovascular disease DALYs, ranging to a low of 0% for neonatal disorders and neglected tropical diseases and malaria. In terms of global DALYs in 2013, six risks or clusters of risks each caused more than 5% of DALYs: dietary risks accounting for 11·3 million deaths and 241·4 million DALYs, high systolic blood pressure for 10·4 million deaths and 208·1 million DALYs, child and maternal malnutrition for 1·7 million deaths and 176·9 million DALYs, tobacco smoke for 6·1 million deaths and 143·5 million DALYs, air pollution for 5·5 million deaths and 141·5 million DALYs, and high BMI for 4·4 million deaths and 134·0 million DALYs. Risk factor patterns vary across regions and countries and with time. In sub-Saharan Africa, the leading risk factors are child and maternal malnutrition, unsafe sex, and unsafe water, sanitation, and handwashing. In women, in nearly all countries in the Americas, north Africa, and the Middle East, and in many other high-income countries, high BMI is the leading risk factor, with high systolic blood pressure as the leading risk in most of Central and Eastern Europe and south and east Asia. For men, high systolic blood pressure or tobacco use are the leading risks in nearly all high-income countries, in north Africa and the Middle East, Europe, and Asia. For men and women, unsafe sex is the leading risk in a corridor from Kenya to South Africa.INTERPRETATION: Behavioural, environmental and occupational, and metabolic risks can explain half of global mortality and more than one-third of global DALYs providing many opportunities for prevention. Of the larger risks, the attributable burden of high BMI has increased in the past 23 years. In view of the prominence of behavioural risk factors, behavioural and social science research on interventions for these risks should be strengthened. Many prevention and primary care policy options are available now to act on key risks.FUNDING: Bill & Melinda Gates Foundation.
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| 4. |
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| 5. |
- Li, Haoyuan, et al.
(author)
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Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source
- 2020
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In: Scientific Data. - : NATURE RESEARCH. - 2052-4463. ; 7:1
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Journal article (peer-reviewed)abstract
- Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 mu m x 1.7 mu m full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.
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| 6. |
- Aragon, Santiago, et al.
(author)
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ACE of Spades in the IoT Security Game: A Flexible IPsec Security Profile for Access Control
- 2018
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Conference paper (peer-reviewed)abstract
- The Authentication and Authorization for ConstrainedEnvironments (ACE) framework provides fine-grainedaccess control in the Internet of Things, where devices areresource-constrained and with limited connectivity. The ACEframework defines separate profiles to specify how exactlyentities interact and what security and communication protocolsto use. This paper presents the novel ACE IPsec profile, whichspecifies how a client establishes a secure IPsec channel witha resource server, contextually using the ACE framework toenforce authorized access to remote resources. The profilemakes it possible to establish IPsec Security Associations, eitherthrough their direct provisioning or through the standardIKEv2 protocol. We provide the first Open Source implementationof the ACE IPsec profile for the Contiki OS and testit on the resource-constrained Zolertia Firefly platform. Ourexperimental performance evaluation confirms that the IPsecprofile and its operating modes are affordable and deployablealso on constrained IoT platforms.
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| 7. |
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| 8. |
- Beck, Matthias, et al.
(author)
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Inequalities for f∗-vectors of Lattice Polytopes
- 2023
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In: Seminaire Lotharingien de Combinatoire. - : Universitat Wien, Fakultat fur Mathematik. - 1286-4889. ; :89
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Journal article (peer-reviewed)abstract
- The Ehrhart polynomial ehrP(n) of a lattice polytope P counts the number of integer points in the n-th dilate of P. The f∗-vector of P, introduced by Felix Breuer in 2012, is the vector of coefficients of ehrP(n) with respect to the binomial coefficient basis (Formula presented.), where d = dimP. Similarly to h/h∗-vectors, the f∗-vector of P coincides with the f-vector of its unimodular triangulations (if they exist). We present several inequalities that hold among the coefficients of f∗-vectors of polytopes. These inequalities resemble striking similarities with existing inequalities for the coefficients of f-vectors of simplicial polytopes; e.g., the first half of the f∗-coefficients increases and the last quarter decreases. Even though f∗-vectors of polytopes are not always unimodal, there are several families of polytopes that carry the unimodality property. We also show that for any polytope with a given Ehrhart h∗-vector, there is a polytope with the same h∗-vector whose f∗-vector is unimodal.
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| 9. |
- Beck, Matthias, et al.
(author)
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Inequalities for f∗-vectors of lattice polytopes
- 2024
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In: Advances in Geometry. - : Walter de Gruyter GmbH. - 1615-715X .- 1615-7168. ; 24:2, s. 141-150
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Journal article (peer-reviewed)abstract
- The Ehrhart polynomial ehr(P)(n) of a lattice polytope P counts the number of integer points in the n-th dilate of P. The f*-vector of P, introduced by Felix Breuer in 2012, is the vector of coefficients of ehr(P)(n) with respect to the binomial coefficient basis {((n-1)(0)),((n-1)(1)),& mldr;,((n-1)(d))}, where d = dim P. Similarly to h/h*-vectors, the f*-vector of P coincides with the f-vector of its unimodular triangulations (if they exist). We present several inequalities that hold among the coefficients of f*-vectors of lattice polytopes. These inequalities resemble striking similarities with existing inequalities for the coefficients of f-vectors of simplicial polytopes; e.g., the first half of the f*-coefficients increases and the last quarter decreases. Even though f*-vectors of polytopes are not always unimodal, there are several families of polytopes that carry the unimodality property. We also show that for any polytope with a given Ehrhart h*-vector, there is a polytope with the same h*-vector whose f*-vector is unimodal.
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| 10. |
- Beckerle, Matthias, et al.
(author)
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Interactive Rule Learning for Access Control : Concepts and Design
- 2011
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In: International Journal on Advances in Intelligent Systems. - : International Academy, Research and Industry Association (IARIA). - 1942-2679. ; 4:3-4, s. 234-244
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Journal article (peer-reviewed)abstract
- Nowadays the majority of users are unable toproperly configure security mechanisms mostly because theyare not usable for them. To reach the goal of having usable security mechanisms, the best solution is to minimize the amount of user interactions and simplify configuration tasks. Automation is a proper solution for minimizing the amount of user interaction. Fully automated security systems are possible for most security objectives, with the exception ofthe access control policy generation. Fully automated accesscontrol policy generation is currently not possible because individual preferences must be taken into account and, thus, requires user interaction. To address this problem we proposea mechanism that assists users to generate proper accesscontrol rule sets that reflect their individual preferences. We name this mechanism Interactive Rule Learning for AccessControl (IRL). IRL is designed to generate concise rule setsfor Attribute-Based Access Control (ABAC). The resulting approach leads to adaptive access control rule sets that can be used for so called smart products. Therefore, we first describe the requirements and metrics for usable access control rulesets for smart products. Moreover, we present the design of asecurity component which implements, among other security functionalities, our proposed IRL on ABAC. This design is currently being implemented as part of the ICT 7th Framework Programme SmartProducts of the European Commission.
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