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| 2. |
- Chng, Kern Rei, et al.
(författare)
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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
- 2020
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 26, s. 941-951
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Tidskriftsartikel (refereegranskat)abstract
- Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections. Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.
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| 3. |
- Danko, David, et al.
(författare)
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A global metagenomic map of urban microbiomes and antimicrobial resistance
- 2021
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 184:13, s. 3376-3393
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Tidskriftsartikel (refereegranskat)abstract
- We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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| 4. |
- Lumpkin, A. H., et al.
(författare)
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Evidence for microbunching "sidebands" in a saturated free-electron laser using coherent optical transition radiation
- 2002
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Ingår i: Physical Review Letters. - 1079-7114. ; 88:23, s. 4-4
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Tidskriftsartikel (refereegranskat)abstract
- We report the first measurements of z -dependent coherent optical transition radiation (COTR) due to electron-beam microbunching at high gains (>10(4) ) including saturation of a self-amplified spontaneous emission free-electron laser (FEL). In these experiments the fundamental wavelength was near 530 nm, and the COTR spectra exhibit the transition from simple spectra to complex spectra (5% spectral width) after saturation. The COTR intensity growth and angular distribution data are reported as well as the evidence for transverse spectral dependencies and an "effective" core of the beam being involved in microbunching.
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| 5. |
- Novak, R., et al.
(författare)
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Robotic fluidic coupling and interrogation of multiple vascularized organ chips
- 2020
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Ingår i: Nature Biomedical Engineering. - : Nature Research. - 2157-846X.
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Tidskriftsartikel (refereegranskat)abstract
- Organ chips can recapitulate organ-level (patho)physiology, yet pharmacokinetic and pharmacodynamic analyses require multi-organ systems linked by vascular perfusion. Here, we describe an ‘interrogator’ that employs liquid-handling robotics, custom software and an integrated mobile microscope for the automated culture, perfusion, medium addition, fluidic linking, sample collection and in situ microscopy imaging of up to ten organ chips inside a standard tissue-culture incubator. The robotic interrogator maintained the viability and organ-specific functions of eight vascularized, two-channel organ chips (intestine, liver, kidney, heart, lung, skin, blood–brain barrier and brain) for 3 weeks in culture when intermittently fluidically coupled via a common blood substitute through their reservoirs of medium and endothelium-lined vascular channels. We used the robotic interrogator and a physiological multicompartmental reduced-order model of the experimental system to quantitatively predict the distribution of an inulin tracer perfused through the multi-organ human-body-on-chips. The automated culture system enables the imaging of cells in the organ chips and the repeated sampling of both the vascular and interstitial compartments without compromising fluidic coupling.
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| 6. |
- Biedron, Sandra G., et al.
(författare)
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Measurements of nonlinear harmonic generation at the Advanced Photon Source's SASE FEL
- 2002
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Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 483:1-2, s. 94-100
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Tidskriftsartikel (refereegranskat)abstract
- SASE saturation was recently achieved at the Advanced Photon Source's SASE FFL in the low-energy undulator test line at 530 nm and 385 urn. The electron beam microbunching becomes more and more prominent until saturation is achieved. This bunching causes nonlinear harmonic emission that extends the usefulness of a SASE system in achieving shorter FEL wavelengths for the same electron beam energy. We have investigated the intensity of the fundamental and second harmonic undulator radiation as a function of distance along the undulator line and present the experimental results and compare them to numerical simulations. In addition, we have measured the single-shot second harmonic spectra as well as the simultaneous fundamental and second harmonic spectra and present the experimental results. (C) 2002 Elsevier Science B.V. All riudits reserved.
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| 7. |
- Herland, Anna, et al.
(författare)
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Quantitative prediction of human pharmacokinetic responses to drugs via fluidically coupled vascularized organ chips
- 2020
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Ingår i: Nature Biomedical Engineering. - : Springer Science and Business Media LLC. - 2157-846X. ; 4:4, s. 421-436
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Tidskriftsartikel (refereegranskat)abstract
- Analyses of drug pharmacokinetics (PKs) and pharmacodynamics (PDs) performed in animals are often not predictive of drug PKs and PDs in humans, and in vitro PK and PD modelling does not provide quantitative PK parameters. Here, we show that physiological PK modelling of first-pass drug absorption, metabolism and excretion in humans—using computationally scaled data from multiple fluidically linked two-channel organ chips—predicts PK parameters for orally administered nicotine (using gut, liver and kidney chips) and for intravenously injected cisplatin (using coupled bone marrow, liver and kidney chips). The chips are linked through sequential robotic liquid transfers of a common blood substitute by their endothelium-lined channels (as reported by Novak et al. in an associated Article) and share an arteriovenous fluid-mixing reservoir. We also show that predictions of cisplatin PDs match previously reported patient data. The quantitative in-vitro-to-in-vivo translation of PK and PD parameters and the prediction of drug absorption, distribution, metabolism, excretion and toxicity through fluidically coupled organ chips may improve the design of drug-administration regimens for phase-I clinical trials.
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| 8. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 9. |
- Lewellen, JW, et al.
(författare)
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Present status and recent results from the APS SASE FEL
- 2002
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Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 483:1-2, s. 40-45
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Tidskriftsartikel (refereegranskat)abstract
- The Low-Energy Undulator Test Line (LEUTL) at the Advanced Photon Source, Argonne National Laboratory, is intended to demonstrate the basic operation of a SASE-based free-electron laser. Goals include comparison of experimental results With theoretical predictions and scaling laws, identification of problems relevant to fourth-generation light source construction and operation and the means of addressing them, the development of operational and diagnostic techniques to optimize SASE FEL performance and increase repeatability from run to run. and performance of initial pioneering experiments capable of exploiting the unique properties of the laser. The basic layout and operational philosophy of the LEUTL experiment is presented. A summary of past results, including saturation, is reviewed, and a description of recent results is presented. We conclude with future plans, which include pressing to shorter wavelengths and incorporating user experiments into the LEUTL experimental program.
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| 10. |
- Milton, Debra L., 1956-, et al.
(författare)
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Low risk for microbial contamination of syringe and tube feeding bag surfaces after multiple reuses with home blenderized tube feeding
- 2022
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Ingår i: Nutrition in clinical practice. - : John Wiley & Sons. - 0884-5336 .- 1941-2452. ; 37:4, s. 907-912
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Tidskriftsartikel (refereegranskat)abstract
- Background: Guidelines for the reuse of enteral tube feeding (ETF) equipment guidelines are limited to manufacturer recommendations. ETF equipment reuse studies are needed as the enteral population has increased, along with blenderized tube feeding (BTF).Methods: This experiment tested microbial contamination of a reusable gravity feeding bag and syringe after 15 BTF reuses and cleanings. Eight bags and syringes were filled with the BTF, held at room temperature for 20 min, and then emptied, washed, and air dried. After the last air drying, the inner surfaces of the bag and syringe were swabbed, and aerobic microbial counts were performed using serial dilutions and plate counts.Results: The microbial counts for all syringes and six bags were <1 colony-forming unit (CFU)/cm2; one bag was <5 CFU/cm2 and one bag was 12.5 CFU/cm2. No legal guidelines for surface cleanliness exist for the food sector. Several studies propose a safe microbial level to be <2.5 CFU/cm2, and the European Commission recommended <10 CFU/cm2. Based on these proposed guidelines, microbial counts of all syringes and seven bags were within the proposed guidelines, except for one bag just above 10 CFU/cm2.Conclusion: The feeding bag used in this study may be used multiple times for BTF with a reduced risk of microbial contamination when manufacturer's cleaning guidelines are followed. Although bolus tube feeding is an off-label use for syringes, they are frequently used for BTF, and in this study the cleaning after 15 uses over 5 days was effective to reduce microbial counts.
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