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| 2. |
- Buckley, Jeffrey, 1992-, et al.
(author)
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An assessment of the transparency of contemporary technology education research employing interview-based methodologies
- 2021
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In: International journal of technology and design education. - : Springer Nature. - 0957-7572 .- 1573-1804.
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Journal article (peer-reviewed)abstract
- A high level of transparency in reported research is critical for several reasons, such as ensuring an acceptable level of trustworthiness and enabling replication. Transparency in qualitative research permits the identification of specific circumstances which are associated with findings and observations. Thus, transparency is important for the repeatability of original studies and for explorations of the transferability of original findings. There has been no investigation into levels of transparency in reported technology education research to date. With a position that increasing transparency would be beneficial, this article presents an analysis of levels of transparency in contemporary technology education research studies which employed interviews within their methodologies, and which were published within the International Journal of Technology and Design Education and Design and Technology Education: An International Journal (n = 38). The results indicate room for improvement, especially in terms of documenting researcher positionality, determinations of data saturation, and how power imbalances were managed. A discussion is presented on why it is important to improve levels of transparency in reported studies, and a guide on areas to make transparent is presented for qualitative and quantitative research.
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| 3. |
- Chng, Kern Rei, et al.
(author)
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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
- 2020
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In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 26, s. 941-951
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Journal article (peer-reviewed)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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| 5. |
- Danko, David, et al.
(author)
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A global metagenomic map of urban microbiomes and antimicrobial resistance
- 2021
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In: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 184:13, s. 3376-3393
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Journal article (peer-reviewed)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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| 6. |
- Fouquet, Antoine, et al.
(author)
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Integrative species delimitation and biogeography of the Rhinella margaritifera species group (Amphibia, Anura, Bufonidae) suggest an intense diversification throughout Amazonia during the last 10 million years
- 2024
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In: Systematics and Biodiversity. - 1477-2000. ; 22:1
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Journal article (peer-reviewed)abstract
- The accumulation of studies delimiting species in Amazonia has not only shed light on the patterns of its outstanding species richness but also allowed a better understanding of the processes of diversification within this immense region. Nevertheless, vast knowledge gaps remain even for prominent anuran species complexes, such as the Rhinella margaritifera species group. This clade of toads comprises 23 valid species-level taxa, mainly distributed in Amazonia but also in South America’s Dry Diagonal and Atlantic and trans-Andean rainforests. Species boundaries and taxonomy in this group are notoriously complex, with studies suggesting the existence of several unnamed species. Available phylogenetic information suggests an Andean-western Amazonian origin of the group with subsequent diversification within Amazonian lowlands during the last 10 Myr and secondary dispersals into other Neotropical regions. To further test this biogeographic scenario and improve knowledge on species diversity, we used an unprecedentedly large mtDNA sampling (>800 16S sequences) across the clade’s distribution and comprising all but one described species. We delimited 54 Molecular Operational Taxonomic Units, which we tested further based on patterns of variation of a nuclear locus and acoustic and morphological data. This approach confirmed the existence of at least 25 candidate species, 19 of which correspond to currently recognized taxa whereas 30 remained ‘unconfirmed’. Our results clarify the taxonomic status of some species but also suggest multiple introgression events that blur some mtDNA-based species boundaries. Lastly, to provide a temporal framework for the clade’s diversification, we generated a time-calibrated phylogenetic tree based on a mitogenomic matrix, which confirmed a Miocene (∼9 Ma) western Amazonian origin and six major clades in the group, each having initially diversified in different regions within Amazonia. Most of these clades have later dispersed throughout Amazonia during the establishment of the modern Amazonian hydrographic system, i.e., in the last 6 Myr.
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| 7. |
- Fumes, R. A., et al.
(author)
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Petrochronology of high-pressure granulite facies rocks from Southern Brasilia Orogen, SE Brazil: Combining quantitative compositional mapping, single-element thermometry and geochronology
- 2022
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In: Journal of Metamorphic Geology. - : Wiley. - 0263-4929 .- 1525-1314. ; 40:3, s. 517-552
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Journal article (peer-reviewed)abstract
- We use a combination of several in situ techniques to assess the P-T-t path of high-pressure granulites from the Passos Nappe in the Southern Brasilia Orogen (SE Brazil). Quantitative element mapping and single-element thermometers (Zr-in-rutile and Ti-in-quartz) are coupled with P-T pseudosections and monazite and rutile dating. Compositional and temperature maps, based on cathodoluminescence mapping and in situ analyses of Ti-in-quartz, are presented as a novel approach to evaluate crystallization temperature. The studied rocks have a pelitic protolith and record a peak pressure assemblage of garnet + kyanite + rutile + K-feldspar + quartz + melt +/- plagioclase that formed at similar to 830 degrees C and 1.2 GPa. Retrograde conditions of similar to 560 degrees C and 0.6 GPa are determined based on the grossular content of garnet and the crystallization of biotite and ilmenite. Metamorphic peak conditions occurred ca. 635 Ma, according to monazite dating, with a younger date of ca. 615 Ma associated with later kyanite crystallization. Rutile ages of ca. 590 Ma are linked to the late retrograde stage (at similar to 600 degrees C). Results show that the distribution of Ti-in-quartz is heterogeneous, decreasing in abundance towards the rim of crystals, though the higher temperatures constrained with Ti-in-quartz thermometry are broadly consistent with peak conditions. The peak pressure conditions are consistent with continental collision setting in the Southern Brasilia Orogen and were followed by an early cooling/decompression stage and then by a slow cooling during exhumation and transport to shallower crustal levels.
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| 8. |
- Glechner, T., et al.
(author)
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Correlation between fracture characteristics and valence electron concentration of sputtered Hf-C-N based thin films
- 2020
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In: Surface & Coatings Technology. - : Elsevier BV. - 0257-8972 .- 1879-3347. ; 399
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Journal article (peer-reviewed)abstract
- Hard protective coating materials based on transition metal nitrides and carbides typically suffer from limited fracture tolerance. To further tune these properties non-metal alloying - substituting C with N - has been proven favorable for magnetron sputtered Hf-C-N based thin films. A theoretically predicted increase in valence electron concentration (from 8.0 to 9.0 e/f.u. from Hf-C to Hf-N) through nitrogen alloying lead to an increase in fracture toughness (K-IC obtained during in-situ SEM cantilever bending) from 1.89 +/- 0.15 to 2.33 +/- 0.18 MPa.m(1/2) for Hf0.43C0.57 to Hf0.35C0.30N0.35, respectively. The hardness remains close to the super-hard regime with values of 37.8 +/- 2.1 to 39.9 +/- 2.7 GPa for these specific compositions. Already the addition of small amounts of nitrogen, while sputtering a ceramic Hf-C target, leads to a drastic increase of nitrogen on the non-metallic sublattice for fcc single phased structured HfC1-xNx films, where x = N/(C + N). The here obtained results also provide experimental proof for the correlation between fracture characteristics and valence electron concentration.
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| 9. |
- Moraes Holst, Luiza, et al.
(author)
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Downregulated Mucosal Autophagy, Alpha Kinase-1 and IL-17 Signaling Pathways in Active and Quiescent Ulcerative Colitis
- 2022
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In: Clinical and Experimental Gastroenterology. - : DOVE MEDICAL PRESS LTD. - 1178-7023. ; 15, s. 129-144
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Journal article (peer-reviewed)abstract
- Background: Improved mucosal immune profiling in active and quiescent colonic inflammatory bowel disease (IBD) is needed to develop therapeutic options for treating and preventing flares. This study therefore aimed to provide a comprehensive mucosal characterization with emphasis on immunological host response of patients with active ulcerative colitis (UC active), UC during remission (UC remission) and active colonic Crohn's disease (CD active).Methods: Colonic biopsies from 47 study subjects were collected for gene expression and pathway analyses using the NanoString host-response panel, including 776 genes and 56 immune-related pathways.Results: The majority of mucosal gene expression and signaling pathway scores were increased in active IBD (n=27) compared to healthy subjects (n=10). However, both active IBD and UC remission (n=10) demonstrated decreased gene expression and signaling pathway scores related to autophagy, alpha kinase-1 and IL-17 signaling pathways compared to healthy subjects. Further, UC remission was characterized by decreased scores of several signaling pathways linked to homeostasis along with increased mononuclear cell migration pathway score as compared to healthy subjects. No major differences in the colonic mucosal gene expression between CD active (n=7) and UC (n=20) active were observed.Conclusion: This study indicates that autophagy, alpha kinase-1 and IL-17 signaling pathways are persistently downregulated in UC irrespective of disease activity. Further, UC patients in remission present a unique mucosal environment, potentially preventing patients from reaching and sustaining true homeostasis. These findings may enable better comprehension of the remitting and relapsing pattern of colonic IBD and guide future treatment and prevention of flares.
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