| 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. |
- Huang, Yanyan, et al.
(författare)
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A 4-year study of avian influenza virus prevalence and subtype diversity in ducks of Newfoundland, Canada.
- 2013
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Ingår i: Canadian journal of microbiology (Print). - : Canadian Science Publishing. - 0008-4166 .- 1480-3275. ; 59:10, s. 701-708
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Tidskriftsartikel (refereegranskat)abstract
- The island of Newfoundland, Canada, is at the eastern edge of North America and has migratory bird connections with the continental mainland as well as across the North Atlantic Ocean. Here, we report a 4-year avian influenza virus (AIV) epidemiological study in ducks in the St. John's region of Newfoundland. The overall prevalence of AIV detection in ducks during this study was 7.2%, with American Black Ducks contributing the vast majority of the collected samples and the AIV positives. The juvenile ducks showed a significantly higher AIV detection rate (10.6%) compared with adults (3.4%). Seasonally, AIV prevalence rates were higher in the autumn (8.4%), but positives were still detected in the winter (4.6%). Preliminary serology tests showed a high incidence of previous AIV infection (20/38, 52.6%). A total of 43 viruses were characterized for their HA-NA or HA subtypes, which revealed a large diversity of AIV subtypes and little recurrence of subtypes from year to year. Investigation of the movement patterns of ducks in this region showed that it is a largely non-migratory duck population, which may contribute to the observed pattern of high AIV subtype turnover. Phylogenetic analysis of 4 H1N1 and one H5N4 AIVs showed these viruses were highly similar to other low pathogenic AIV sequences from waterfowl in North America and assigned all gene segments into American-avian clades. Notably, the H1N1 viruses, which were identified in consecutive years, possessed homologous genomes. Such detection of homologous AIV genomes across years is rare, but indicates the role of the environmental reservoir in viral perpetuation.
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| 3. |
- Huang, Yanyan, et al.
(författare)
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Genetic structure of avian influenza viruses from ducks of the Atlantic flyway of North America.
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Wild birds, including waterfowl such as ducks, are reservoir hosts of influenza A viruses. Despite the increased number of avian influenza virus (AIV) genome sequences available, our understanding of AIV genetic structure and transmission through space and time in waterfowl in North America is still limited. In particular, AIVs in ducks of the Atlantic flyway of North America have not been thoroughly investigated. To begin to address this gap, we analyzed 109 AIV genome sequences from ducks in the Atlantic flyway to determine their genetic structure and to document the extent of gene flow in the context of sequences from other locations and other avian and mammalian host groups. The analyses included 25 AIVs from ducks from Newfoundland, Canada, from 2008-2011 and 84 available reference duck AIVs from the Atlantic flyway from 2006-2011. A vast diversity of viral genes and genomes was identified in the 109 viruses. The genetic structure differed amongst the 8 viral segments with predominant single lineages found for the PB2, PB1 and M segments, increased diversity found for the PA, NP and NS segments (2, 3 and 3 lineages, respectively), and the highest diversity found for the HA and NA segments (12 and 9 lineages, respectively). Identification of inter-hemispheric transmissions was rare with only 2% of the genes of Eurasian origin. Virus transmission between ducks and other bird groups was investigated, with 57.3% of the genes having highly similar (≥99% nucleotide identity) genes detected in birds other than ducks. Transmission between North American flyways has been frequent and 75.8% of the genes were highly similar to genes found in other North American flyways. However, the duck AIV genes did display spatial distribution bias, which was demonstrated by the different population sizes of specific viral genes in one or two neighbouring flyways compared to more distant flyways.
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| 4. |
- Huang, Yanyan, et al.
(författare)
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Perpetuation and reassortment of gull influenza A viruses in Atlantic North America
- 2014
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Ingår i: Virology. - : Elsevier BV. - 0042-6822 .- 1096-0341. ; 456-457, s. 353-363
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Tidskriftsartikel (refereegranskat)abstract
- Gulls are important hosts of avian influenza A viruses (AIVs) and gull AIVs often contain gene segments of mixed geographic and host lineage origins. In this study, the prevalence of AIV in gulls of Newfoundland, Canada from 2008 to 2011 was analyzed. Overall prevalence was low (30/1645, 1.8%) but there was a distinct peak of infection in the fall. AIV seroprevalence was high in Newfoundland gulls, with 50% of sampled gulls showing evidence of previous infection. Sequences of 16 gull AIVs were determined and analyzed to shed light on the transmission, reassortment and persistence dynamics of gull AIVs in Atlantic North America. Intercontinental and waterfowl lineage reassortment was prevalent. Of particular note were a wholly Eurasian AIV and another with an intercontinental reassortant waterfowl lineage virus. These patterns of geographic and inter-host group transmission highlight the importance of characterization of gull AIVs as part of attempts to understand global AIV dynamics.
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| 5. |
- Kristan, Matej, et al.
(författare)
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The Ninth Visual Object Tracking VOT2021 Challenge Results
- 2021
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Ingår i: 2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2021). - : IEEE COMPUTER SOC. - 9781665401913 ; , s. 2711-2738
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2021 is the ninth annual tracker benchmarking activity organized by the VOT initiative. Results of 71 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in recent years. The VOT2021 challenge was composed of four sub-challenges focusing on different tracking domains: (i) VOT-ST2021 challenge focused on short-term tracking in RGB, (ii) VOT-RT2021 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2021 focused on long-term tracking, namely coping with target disappearance and reappearance and (iv) VOT-RGBD2021 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2021 dataset was refreshed, while VOT-RGBD2021 introduces a training dataset and sequestered dataset for winner identification. The source code for most of the trackers, the datasets, the evaluation kit and the results along with the source code for most trackers are publicly available at the challenge website(1).
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| 6. |
- Li, Feiran, 1993, et al.
(författare)
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Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Eukaryotic cells are used as cell factories to produce and secrete multitudes of recombinant pharmaceutical proteins, including several of the current top-selling drugs. Due to the essential role and complexity of the secretory pathway, improvement for recombinant protein production through metabolic engineering has traditionally been relatively ad-hoc; and a more systematic approach is required to generate novel design principles. Here, we present the proteome-constrained genome-scale protein secretory model of yeast Saccharomyces cerevisiae (pcSecYeast), which enables us to simulate and explain phenotypes caused by limited secretory capacity. We further apply the pcSecYeast model to predict overexpression targets for the production of several recombinant proteins. We experimentally validate many of the predicted targets for alpha-amylase production to demonstrate pcSecYeast application as a computational tool in guiding yeast engineering and improving recombinant protein production. Due to the complexity of the protein secretory pathway, strategy suitable for the production of a certain recombination protein cannot be generalized. Here, the authors construct a proteome-constrained genome-scale protein secretory model for yeast and show its application in the production of different misfolded or recombinant proteins.
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| 7. |
- Wille, Michelle, et al.
(författare)
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Evaluation of seabirds in Newfoundland and Labrador, Canada, as hosts of influenza A viruses.
- 2014
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Ingår i: Journal of Wildlife Diseases. - : Wildlife Disease Association. - 0090-3558 .- 1943-3700. ; 50:1, s. 98-103
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Tidskriftsartikel (refereegranskat)abstract
- Influenza A viruses infect a wide range of hosts, including many species of birds. Avian influenza A virus (AIV) infection appears to be most common in Anseriformes (ducks, geese, and swans) and some Charadriiformes (shorebirds and gulls), but many other birds also serve as hosts of AIV. Here, we evaluated the role of seabirds as hosts for AIV. We tested 3,160 swab samples from 13 seabird species between May 2008 and December 2011 in Newfoundland and Labrador, Canada. We also tested 156 serum samples for evidence of previous infection of AIV in Common Murres (Uria aalge) and Atlantic Puffins (Fratercula arctica). Avian influenza A virus was detected in breeding Common Murres and nonbreeding Thick-billed Murres (Uria lomvia), and Common Murres also had high antibody prevalence (44%). From these findings, combined with other studies showing AIV infection in murres, we conclude that murres are important for the ecology of AIV. For other species (Razorbill, Alca torda; Leach's Storm-Petrel, Oceanodroma leucorhoa; Black-legged Kittiwake, Rissa tridactyla; Atlantic Puffin) with good coverage (>100 samples) we did not detect AIV. However, serology indicates infection does occur in Atlantic Puffins, with 22% antibody prevalence found. The possibility of virus spread through dense breeding colonies and the long distance movements of these hosts make a more thorough evaluation of the role for seabirds as hosts of AIV important.
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| 8. |
- Zhu, Zhenyu, et al.
(författare)
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Coupling life prediction of bending very high cycle fatigue of completion strings made of different materials using deep wise separable convolution
- 2024
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Ingår i: Fatigue & Fracture of Engineering Materials & Structures. - : WILEY. - 8756-758X .- 1460-2695.
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Tidskriftsartikel (refereegranskat)abstract
- This article predicts bending very high cycle fatigue (VHCF) life of three typical nickel-based alloys SM2550, BG2532, and G3 used for completion strings. Fatigue tests were conducted on the three alloys using an ultrasonic fatigue system at a frequency of 20 kHz. The results showed that the fatigue strength ranges of the three alloys were markedly different, reflecting their different sensitivities to fatigue loading. Scanning electron microscope observations revealed numerous fatigue crack origins with internal decohesion in the fatigue source region. To achieve unified prediction of the fatigue life for the three alloys, a prediction model based on deep learning was built with inputs including fatigue initiation quantity, cleavage facet size, and other fatigue fracture characteristics. It was found that single source feature was insufficient to obtain satisfactory prediction accuracy for all alloys, while multifeature coupling integration could significantly improve the prediction precision, enabling reliable prediction of alloy fatigue life. This study provides new insights into bending VHCF life prediction. This article predicts bending VHCF life for three completion strings. Bending VHCF life model utilizing deep wise separable convolution was established. Deep learning can effectively integrate with bending VHCF analyses.
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| 9. |
- Zhu, Zhenyu, et al.
(författare)
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Origin of prestrain-induced cyclic-strain hardening: Multi-scale experimental characterizations and simulations of 7075 aluminum alloy
- 2024
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Ingår i: Materials & design. - : ELSEVIER SCI LTD. - 0264-1275 .- 1873-4197. ; 238
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Tidskriftsartikel (refereegranskat)abstract
- The influence of prefabricated dislocation features induced by rate dependent prestrain on the post-cyclic process in 7075 aluminum alloy exhibits significant variations, which are of great importance in terms of concerns, designs, and discoveries. Considering strain rate dependent prestrain provides diversified hardening stimuli for the subsequent cyclic process. The maximum cyclic stress in the post-cyclic stage was maintained at the same level as the prestress with strain rates ranging from 10-4s-1 to 10-1s-1. Subsequently, by adjusting post-cycling stress amplitude, research was conducted on quasi-plastic amplitude cycle (QPC) and low plasticity amplitude cycle (LPC) loading conditions. Through experimental mechanism analysis, as well as verification through molecular dynamics and crystal plasticity simulations, prestrain induced by rapid strain rates enhanced the hardening during QPC, stemming from the effects of matrix reconstruction strengthening and wavy structured grain boundaries. However, prestrain induced by slow strain rates promoted the hardening during LPC, primarily arising from the non-uniform crystal structures within individual grains, which was achieved through the complex sub-crystal clusters at grain boundaries, along with intracrystal orderly slipping lattice. These findings offer new insights for the optimization of microstructural design through dislocation engineering.
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