| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)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. |
- Lensink, Marc F., et al.
(författare)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 3. |
- Zou, Yonggang, et al.
(författare)
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Effective polymerization of C60 in SWNTs under high pressure and simultaneous UV light irradiation
- 2007
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Ingår i: Acta Physica Sinica (Wuli Xuebao). - 1000-3290. ; 56:9, s. 5172-5175
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Tidskriftsartikel (refereegranskat)abstract
- The C-60 @ SWNT ( peapod) samples were prepared by the vapor diffusion method. Polymerization of C60 molecules in single walled carbon nanotubes (SWNTs) under high pressure and simultaneous irradiation of UV laser (325 nm) has been carried out for the first time by using diamond anvil cell. Raman spectra of the peapod samples decompressed from high pressure indicated that C60 molecules form one-dimensional orthorhombic polymer in SWNTs under UV laser irradiation at a high pressure of 21.5 GPa, which is lower than that for the polymerization of samples induced by high pressure only. The polymerization is an irreversible phase transition in the peapod.
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| 4. |
- Bi, Meihua, et al.
(författare)
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Client scheduling and bandwidth slicing for multiple federated learning tasks over multiple passive optical networks
- 2024
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Ingår i: Computer Networks. - 1389-1286. ; 243
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Tidskriftsartikel (refereegranskat)abstract
- Federated Learning (FL) has attracted extensive attention in facilitating emerging edge intelligence applications for its inherent advantages of ensuring data security and privacy. Especially in the edge computing networks connected by Passive Optical Network (PON) system, FL is introduced to enable applications like autonomous driving, intelligent manufacturing, and precision medicine. However, in this system, the FL deployment over PON inevitably faces challenges induced by the conflict between a large volume of model data with the restrict latency limitation and the confined bandwidth resource of PON, especially for the multiple FL tasks. To address these issues, a novel scheme is proposed for tackling the client distribution and bandwidth allocation problems under the scenario of multiple simultaneous FL tasks supported by the multiple interconnected PON systems, which is consisted of the client scheduling and bandwidth slicing processes. To be specific, an easy-to-implement heuristic algorithm is first performed to assign the client numbers to PONs based on iterative method, with which certain operations are repetitively executed to achieve optimal solutions. And then, the serial bandwidth slicing which adapts the traditional policy, i.e., one-task-per-cycle, to the situation with multiple FL tasks, and parallel slicing with the multi-task-per-cycle, are designed for the investigated system. Furthermore, the simulation system is constructed to verify our method. The corresponding results exhibit that, the largest 43.2 % round time reduction is achieved by client scheduling compared to benchmark without the scheduling. Compared to the benchmark with serial slicing, our scheme can achieve a maximum 50.11 % of the round time decrease. It's also validated that, our proposed client scheduling and parallel bandwidth slicing method can improve the learning efficiency by reducing communication delay, especially for the situation with less client number and smaller FL threshold.
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| 5. |
- Buccolieri, Riccardo, et al.
(författare)
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Drag force rose representing the interaction between urban geometries and wind
- 2021
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Ingår i: 15th ROOMVENT (Roomvent 2020) virtual conference. - 9788894612301 ; , s. 85-88
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Konferensbidrag (refereegranskat)abstract
- The drag force generated by aligned arrays of cubes of different packing density and exposed to different wind directions in a wind tunnel is discussed. Results allowed to build a drag force rose which shows that the drag force increases with increasing packing density till λp = 0.25 for any wind direction. It is also shown that, independent of the packing density, the drag force increases with increases deviation of WD from the perpendicularity.
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| 6. |
- Cehlin, Mathias, Doktor, 1974-, et al.
(författare)
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Towards benchmarking of urban air quality based on homogenous surface emission
- 2023
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Ingår i: Results in Engineering (RINENG). - : Elsevier. - 2590-1230. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Here, it is presented a possible methodology and experimental model for benchmarking of air quality in cities. The concept behind the methodology is that a city’s inherent structure affects the potential for contaminant removal due to the resistance it poses to inflow. The approach is based on homogenous emission across the street surface network, representing a worst-case situation. Different levels of complexity can be used for benchmarking, making it valuable for evaluating different layouts. Additionally, an urban ventilation index suitable for these kinds of experimental studies has been suggested.
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| 7. |
- Cehlin, Mathias, Doktor, 1974-, et al.
(författare)
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Urban Morphology and City Ventilation
- 2020
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Konferensbidrag (refereegranskat)abstract
- The purpose of the paper is to examine the relation between urban morphology, wind direction and air flow rates. In the study a highly idealized city model was used consisting of a circular block divided into two or four equally large sectors. Wind tunnel experiments and CFD predictions have been conducted. The interaction between the atmospheric boundary layer and a city is considered to be both a function of the overall shape and the internal resistance to the flow caused by the friction when the wind flows over the urban surfaces. Flow along the streets is generated by pressure differences. In the wind tunnel, velocity measurements have been recorded in the streets at several points and pressure on the ground was registered in 400 points. The wind tunnel measurements were used to validate the CFD model. The CFD predictions provided complete flow and pressure fields for different configurations and wind directions. The flow balance is presented considering both the horizontal air flow and the vertical air flow (subsidence and updraft). Special attention was on the pressure distribution at ground level (pressure footprint), which is believed to provide valuable information that can be used for qualitative city ventilation analyses.
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| 8. |
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| 9. |
- Gemmell, Neil J., et al.
(författare)
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The tuatara genome reveals ancient features of amniote evolution
- 2020
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 584:7821, s. 403-409
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Tidskriftsartikel (refereegranskat)abstract
- The tuatara (Sphenodon punctatus)—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2—is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
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| 10. |
- Hou, Yuanyuan, et al.
(författare)
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Comparative study of pressure-induced polymerization of C60 nanorods and single crystals
- 2007
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Ingår i: Journal of Physics Condensed Matter. - Bristol : Institute of Physics. - 0953-8984 .- 1361-648X. ; 19:42, s. 425207-
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we report a comparative study of pressure-induced polymerization in C60 nanorods and bulk single crystals, treated simultaneously under various pressures and temperatures in the same experiment. For both materials, orthorhombic, tetragonal and rhombohedral phases have been produced under high pressure and high temperature. The structures have been identified and compared between the two sample types by Raman and photoluminescence spectroscopy. There are differences between the Raman and photoluminescence spectra from the two types of materials for all polymeric phases, but especially for the tetragonal phase. From the comparison between nanorods and bulk samples, we tentatively assign photoluminescence peaks for various polymeric phases.
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