| 1. |
- 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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| 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. |
- Soler, J. M., et al.
(författare)
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Predictive Modeling of a Simple Field Matrix Diffusion Experiment Addressing Radionuclide Transport in Fractured Rock. Is It So Straightforward?
- 2022
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Ingår i: Nuclear Technology. - : Informa UK Limited. - 0029-5450 .- 1943-7471. ; 208:6, s. 1059-1073
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Tidskriftsartikel (refereegranskat)abstract
- The SKB GroundWater Flow and Transport of Solutes Task Force is an international forum in the area of conceptual and numerical modeling of groundwater flow and solute transport in fractured rocks relevant for the deep geological disposal of radioactive waste. Two in situ matrix diffusion experiments in crystalline rock (gneiss) were performed at POSIVA’s ONKALO underground facility in Finland. Synthetic groundwater containing several conservative and sorbing radiotracers was injected at one end of a borehole interval and flowed along a thin annulus toward the opposite end. Several teams performed predictive modeling of the tracer breakthrough curves using “conventional” modeling approaches (constant diffusion and sorption in the rock, no or minimum rock heterogeneity). Supporting information, derived from small-scale laboratory experiments, was provided. The teams were free to implement different concepts, use different codes, and apply the transport and retention parameters that they considered to be most suited (i.e., not a benchmark exercise). The main goal was the comparison of the different sets of results and the analysis of the possible differences for this relatively simple experimental setup with a well-defined geometry. Even though the experiment was designed to study matrix diffusion, the calculated peaks of the breakthrough curves were very sensitive to the assumed magnitude of dispersion in the borehole annulus. However, given the very different timescales for advection and matrix diffusion, the tails of the curves provided information concerning diffusion and retention in the rock matrix regardless of the magnitude of dispersion. In addition, although the task was designed to be a blind modeling exercise, the model results have also been compared to the measured experimental breakthroughs. Experimental results tend to show relatively small activities, wide breakthroughs, and early first arrivals, which are somewhat similar to model results using large dispersivity values.
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| 4. |
- Galofré, Mireia, et al.
(författare)
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GABA(A) receptor and cell membrane potential as functional endpoints in cultured neurons to evaluate chemicals for human acute toxicity
- 2010
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Ingår i: Neurotoxicology and Teratology. - : Elsevier BV. - 0892-0362 .- 1872-9738. ; 32, s. 52-61
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Tidskriftsartikel (refereegranskat)abstract
- Toxicity risk assessment for chemical-induced human health hazards relies mainly on data obtained from animal experimentation, human studies and epidemiology. In vitro testing for acute toxicity based on cytotoxicity assays predicts 70 - 80% of rodent and human toxicity. The nervous system is particularly vulnerable to chemical exposure which may result in different toxicity features. Acute human toxicity related to adverse neuronal function is usually a result of over-excitation or depression of the nervous system. The major molecular and cellular mechanisms involved in such reactions include GABAergic, glutamatergic and cholinergic neurotransmission, regulation of cell and mitochondrial membrane potential, and those critical for maintaining central nervous system functionality, such as controlling cell energy. In this work, a set of chemicals that are used in pharmacy, industry, biocide treatments or are often abused by drug users are tested for their effects on GABA(A) receptor activity, GABA and glutamate transport, cell membrane potential and cell viability in primary neuronal cultures. GABA(A) receptor function was inhibited by compounds for which seizures have been observed after severe human poisoning. Commonly abused drugs inhibit GABA uptake but not glutamate uptake. Most neurotoxins altered membrane potential. The GABA(A) receptor, GABA uptake and cell membrane potential assays were those that identified the highest number of chemicals as toxic at low concentrations. These results show that in vitro cell assays may identify compounds that produce acute neurotoxicity in humans, provided that in vitro models expressing neuronal targets relevant for acute neural dysfunctions are used.
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| 5. |
- Ryon, Krista A., et al.
(författare)
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A history of the MetaSUB consortium : Tracking urban microbes around the globe
- 2022
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Ingår i: iScience. - : Cell Press. - 2589-0042. ; 25:11
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Tidskriftsartikel (refereegranskat)abstract
- The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.
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| 6. |
- Schindler, Frank, et al.
(författare)
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Fractional corner charges in spin-orbit coupled crystals
- 2019
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Ingår i: Physical Review Research. - : AMER PHYSICAL SOC. - 2643-1564. ; 1:3
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Tidskriftsartikel (refereegranskat)abstract
- We study two-dimensional spinful insulating phases of matter that are protected by time-reversal and crystalline symmetries. To characterize these phases, we employ the concept of corner charge fractionalization: corners can carry charges that are fractions of even multiples of the electric charge. The charges are quantized and topologically stable as long as all symmetries are preserved. We classify the different corner charge configurations for all point groups, and match them with the corresponding bulk topology. For this we employ symmetry indicators and (nested) Wilson loop invariants. We provide formulas that allow for a convenient calculation of the corner charge from Bloch wave functions and illustrate our results using the example of arsenic and antimony monolayers. Depending on the degree of structural buckling, these materials can exhibit two distinct obstructed atomic limits. We present density functional theory calculations for open flakes to support our findings.
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