| 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. |
- Brooks, Christopher, et al.
(author)
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Rapid and near real-time assessments of population displacement using mobile phone data following disasters: the 2015 Nepal Earthquake
- 2016
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In: Plos Currents. - : Public Library of Science. - 2157-3999. ; 8
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Journal article (peer-reviewed)abstract
- Sudden impact disasters often result in the displacement of large numbers of people. These movements can occur prior to events, due to early warning messages, or take place post-event due to damages to shelters and livelihoods as well as a result of long-term reconstruction efforts. Displaced populations are especially vulnerable and often in need of support. However, timely and accurate data on the numbers and destinations of displaced populations are extremely challenging to collect across temporal and spatial scales, especially in the aftermath of disasters. Mobile phone call detail records were shown to be a valid data source for estimates of population movements after the 2010 Haiti earthquake, but their potential to provide near real-time ongoing measurements of population displacements immediately after a natural disaster has not been demonstrated.Methods: A computational architecture and analytical capacity were rapidly deployed within nine days of the Nepal earthquake of 25th April 2015, to provide spatiotemporally detailed estimates of population displacements from call detail records based on movements of 12 million de-identified mobile phones users.Results: Analysis shows the evolution of population mobility patterns after the earthquake and the patterns of return to affected areas, at a high level of detail. Particularly notable is the movement of an estimated 390,000 people above normal from the Kathmandu valley after the earthquake, with most people moving to surrounding areas and the highly-populated areas in the central southern area of Nepal.Discussion: This analysis provides an unprecedented level of information about human movement after a natural disaster, provided within a very short timeframe after the earthquake occurred. The patterns revealed using this method are almost impossible to find through other methods, and are of great interest to humanitarian agencies.
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| 3. |
- Hoffmann, J. Elis, et al.
(author)
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Mechanisms of Archean crust formation inferred from high-precision HFSE systematics in TTGs
- 2011
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In: Geochimica et Cosmochimica Acta. - : Elsevier BV. - 0016-7037 .- 1872-9533. ; 75:15, s. 4157-4178
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Journal article (peer-reviewed)abstract
- It has been proposed that Archean tonalitic-trondhjemitic-granodioritic magmas (TTGs) formed by melting of mafic crust at high pressures. The residual mineralogy of the TTGs (either (garnet)-amphibolite or rutile-bearing eclogite) is believed to control the trace element budget of TTGs. In particular, ratios of high-field-strength elements (HFSE) can help to discriminate between the different residual lithologies. In order to place constraints on the source mineralogy of TTGs, we performed high-precision HFSE measurements by isotope dilution (Nb, Ta, Zr, Hf) together with Lu-Hf and Sm-Nd measurements on representative, ca. 3.85-2.8 Ga TTGs and related rock types from southern West Greenland, W-India and from the Superior Province. These measurements are complemented by major and trace element data for the TTGs. Texturally homogeneous early Archean (3.85-3.60 Ga old) and Mesoarchean (ca. 3.1-2.8 Ga old) TTGs have both low Ni (<11 ppm) and Cr contents (<20 ppm), indicating that there was little or no interaction with mantle peridotite during ascent. Ratios of Nb/Ta in juvenile Eoarchean TTGs range from ca. 7 to ca. 24, and in juvenile Mesoarchean TTGs from ca. 14 to ca. 27. Even higher Nb/Ta (14-42) were obtained for mig-matitic TTGs and intra-crustal differentiates, most likely mirroring further fractionation of Nb from Ta as a consequence of partial melting, fluid infiltration and migmatisation. In the juvenile TTGs, positive correlations between Nb/Ta and Gd/Yb, La/Yb, Sr/Y, Zr/Sm and Zr/Nb are observed. These compositional arrays are best explained by melting of typical Isua tholeiites in both, the rutile-bearing eclogite stability field (>15 kbar, high Nb/Ta) and the garnet-amphibolite stability field (10-15 kbar, low Nb/Ta). With respect to the low end of Nb/Ta found for TTGs, there is currently some uncertainty between the available experimental datasets for amphibole. Independent of these uncertainties, the TTG compositions found here still require the presence of both endmember residues. A successful geological model for the TTGs therefore has to account for the co-occurrence of both low-and high-Nb/Ta TTGs within the same geologic terrane. An additional feature observed in the Eoarchean samples from Greenland is a systematic co-variation between Nb/Ta and initial epsilon Hf(t), which is best explained by a model where TTG-melting occured at progressively increasing pressures in a pile of tectonically thickened mafic crust. The elevated Nb/Ta in mig-matitic TTGs and intra-crustal differentiates can shed further light on the role of intra-crustal differentiation processes in the global Nb/Ta cycle. Lower crustal melting processes at granulite facies conditions may generate high-Nb/Ta domains in the middle crust, whereas mid-crustal melting at amphibolite facies conditions may account for the low Nb/Ta generally observed in upper crustal rocks.
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| 4. |
- Power, Daniel, et al.
(author)
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Population mobility reductions associated with travel restrictions during the Ebola epidemic in Sierra Leone : Use of mobile phone data
- 2018
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In: International Journal of Epidemiology. - : Oxford University Press (OUP): Policy B - Oxford Open Option D. - 1464-3685 .- 0300-5771. ; 47:5, s. 1562-1570
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Journal article (peer-reviewed)abstract
- Travel restrictions were implementeded on an unprecedented scale in 2015 in Sierra Leone to contain and eliminate Ebola virus disease. However, the impact of epidemic travel restrictions on mobility itself remains difficult to measure with traditional methods. New ‘big data’ approaches using mobile phone data can provide, in near real-time, the type of information needed to guide and evaluate control measures.We analysed anonymous mobile phone call detail records (CDRs) from a leading operator in Sierra Leone between 20 March and 1 July in 2015. We used an anomaly detection algorithm to assess changes in travel during a national ‘stay at home’ lockdown from 27 to 29 March. To measure the magnitude of these changes and to assess effect modification by region and historical Ebola burden, we performed a time series analysis and a crossover analysis.Routinely collected mobile phone data revealed a dramatic reduction in human mobility during a 3-day lockdown in Sierra Leone. The number of individuals relocating between chiefdoms decreased by 31% within 15 km, by 46% for 15–30 km and by 76% for distances greater than 30 km. This effect was highly heterogeneous in space, with higher impact in regions with higher Ebola incidence. Travel quickly returned to normal patterns after the restrictions were lifted.The effects of travel restrictions on mobility can be large, targeted and measurable in near real-time. With appropriate anonymization protocols, mobile phone data should play a central role in guiding and monitoring interventions for epidemic containment.
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| 5. |
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| 6. |
- Wein, Nicolas, et al.
(author)
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Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice
- 2014
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In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 20:9, s. 992-1000
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Journal article (peer-reviewed)abstract
- Most mutations that truncate the reading frame of the DMD gene cause loss of dystrophin expression and lead to Duchenne muscular dystrophy. However, amelioration of disease severity has been shown to result from alternative, translation initiation beginning in DMD exon 6 that leads to expression of a highly functional N-truncated dystrophin. Here we demonstrate that this isoform results from usage of an internal ribosome entry site (IRES) within exon 5 that is glucocorticoid inducible. We confirmed IRES activity by both peptide sequencing and ribosome profiling in muscle from individuals with minimal symptoms despite the presence of truncating mutations. We generated a truncated reading frame upstream of the IRES by exon skipping, which led to synthesis of a functional N-truncated isoform in both human subject derived cell lines and in a new DMD mouse model, where expression of the truncated isoform protected muscle from contraction-induced injury and corrected muscle force to the same level as that observed in control mice. These results support a potential therapeutic approach for patients with mutations within the 5' exons of DMD.
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