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- Öling, S., et al.
(author)
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A human stomach cell type transcriptome atlas
- 2024
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In: BMC Biology. - : Springer Nature. - 1741-7007. ; 22:1
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Journal article (peer-reviewed)abstract
- Background: The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single-cell sequencing-based atlases. Results: Here, we use an integrative correlation analysis method to predict human stomach cell type transcriptome signatures using unfractionated stomach RNAseq data from 359 individuals. We profile parietal, chief, gastric mucous, gastric enteroendocrine, mitotic, endothelial, fibroblast, macrophage, neutrophil, T-cell, and plasma cells, identifying over 1600 cell type-enriched genes. Conclusions: We uncover the cell type expression profile of several non-coding genes strongly associated with the progression of gastric cancer and, using a sex-based subset analysis, uncover a panel of male-only chief cell-enriched genes. This study provides a roadmap to further understand human stomach biology.
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- Angelo, Kristina M., et al.
(author)
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Zika among international travellers presenting to GeoSentinel sites, 2012-2019 : implications for clinical practice
- 2020
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In: Journal of Travel Medicine. - : Oxford University Press. - 1195-1982 .- 1708-8305. ; 27:4
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Journal article (peer-reviewed)abstract
- Introduction: International travellers contribute to the rapid spread of Zika virus (ZIKV) and its sentinel identification globally. We describe ZIKV infections among international travellers seen at GeoSentinel sites with a focus on ZIKV acquired in the Americas and the Caribbean, describe countries of exposure and traveller characteristics, and assess ZIKV diagnostic testing by site. Methods: Records with an international travel-related diagnosis of confirmed or probable ZIKV from January 2012 through December 2019 reported to GeoSentinel with a recorded illness onset date were included to show reported cases over time. Records from March 2016 through December 2019 with an exposure region of the Americas or the Caribbean were included in the descriptive analysis. A survey was conducted to assess the availability, accessibility and utilization of ZIKV diagnostic tests at GeoSentinel sites. Results: GeoSentinel sites reported 525 ZIKV cases from 2012 through 2019. Between 2012 and 2014, eight cases were reported, and all were acquired in Asia or Oceania. After 2014, most cases were acquired in the Americas or the Caribbean, a large decline in ZIKV cases occurred in 2018-19. Between March 2016 and December 2019, 423 patients acquired ZIKV in the Americas or the Caribbean, peak reporting to these regions occurred in 2016 [330 cases (78%)]. The median age was 36 years (range: 3-92); 63% were female. The most frequent region of exposure was the Caribbean (60%). Thirteen travellers were pregnant during or after travel; one had a sexually acquired ZIKV infection. There was one case of fetal anomaly and two travellers with Guillain-Barre syndrome. GeoSentinel sites reported various challenges to diagnose ZIKV effectively. Conclusion: ZIKV should remain a consideration for travellers returning from areas with risk of ZIKV transmission. Travellers should discuss their travel plans with their healthcare providers to ensure ZIKV prevention measures are taken.
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- Hassan, Jamshaidul, et al.
(author)
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Construction of circular quasi rees neighbor designs which can be converted into minimal circular balanced and strongly balanced neighbor designs
- 2023
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In: Communications in Statistics - Theory and Methods. - : Informa UK Limited. - 0361-0926 .- 1532-415X. ; 52:16, s. 5587-5605
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Journal article (peer-reviewed)abstract
- The response of a treatment (direct effect) applied on a given unit may be affected by the treatments applied to its neighboring units (neighbor effects). Neighbor designs are considered robust to neighbor effects. Minimal neighbor designs are economical, therefore, these are preferred by the experimenters. Method of cyclic shifts (Rule I) provides the minimal neighbor designs for odd v (number of treatments). Method of cyclic shifts (Rule II) provides the minimal circular Quasi Rees neighbor designs for v even which are considered to be the good alternate to the minimal neighbor designs. In this article, for every case of v even, minimal circular Quasi Rees neighbor designs are constructed in such a way that these designs can also be converted directly into minimal circular balanced and strongly balanced neighbor designs.
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- Huaraca Huasco, Walter, et al.
(author)
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Fine root dynamics across pantropical rainforest ecosystems
- 2021
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In: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 27:15, s. 3657-3680
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Journal article (peer-reviewed)abstract
- Fine roots constitute a significant component of the net primary productivity (NPP) of forest ecosystems but are much less studied than aboveground NPP. Comparisons across sites and regions are also hampered by inconsistent methodologies, especially in tropical areas. Here, we present a novel dataset of fine root biomass, productivity, residence time, and allocation in tropical old-growth rainforest sites worldwide, measured using consistent methods, and examine how these variables are related to consistently determined soil and climatic characteristics. Our pantropical dataset spans intensive monitoring plots in lowland (wet, semi-deciduous, and deciduous) and montane tropical forests in South America, Africa, and Southeast Asia (n = 47). Large spatial variation in fine root dynamics was observed across montane and lowland forest types. In lowland forests, we found a strong positive linear relationship between fine root productivity and sand content, this relationship was even stronger when we considered the fractional allocation of total NPP to fine roots, demonstrating that understanding allocation adds explanatory power to understanding fine root productivity and total NPP. Fine root residence time was a function of multiple factors: soil sand content, soil pH, and maximum water deficit, with longest residence times in acidic, sandy, and water-stressed soils. In tropical montane forests, on the other hand, a different set of relationships prevailed, highlighting the very different nature of montane and lowland forest biomes. Root productivity was a strong positive linear function of mean annual temperature, root residence time was a strong positive function of soil nitrogen content in montane forests, and lastly decreasing soil P content increased allocation of productivity to fine roots. In contrast to the lowlands, environmental conditions were a better predictor for fine root productivity than for fractional allocation of total NPP to fine roots, suggesting that root productivity is a particularly strong driver of NPP allocation in tropical mountain regions.
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- Nadeem, Muhammad, et al.
(author)
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New generators for minimal circular generalised neighbour designs in blocks of two different sizes
- 2023
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In: Statistics in Transition New Series. - 1234-7655 .- 2450-0291. ; 24:2, s. 85-92
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Journal article (peer-reviewed)abstract
- Minimal neighbour designs (NDs) are used when a response of a treatment (direct effect) is affected by the treatment(s) applied in the neighbouring units. Minimal generalised NDs are preferred when minimal NDs cannot be constructed. Through the method of cyclic shifts (Rule I), the conditions for the existence of minimal circular generalised NDs are discussed, in which v/2 unordered pairs do not appear as neighbours. Certain generators are also developed to obtain minimal circular generalised NDs in blocks of two different sizes, where k2 = 3, 4 and 5. All these designs are constructed using i sets of shifts for k1 and two for k2.
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- Noreen, Khadija, et al.
(author)
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Some important classes of non-directional minimal circular weakly balanced neighbor designs
- 2023
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In: Communications in statistics. Simulation and computation. - 0361-0918 .- 1532-4141. ; , s. 1-10
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Journal article (peer-reviewed)abstract
- Minimal neighbor designs are useful to balance out neighbor effects economically. The method of cyclic shifts provides the construction of these minimal designs in circular blocks only for v odd, where v is the number of treatments to be compared. Minimal circular weakly balanced neighbor designs are used for v even. In this article, two classes of minimal circular weakly balanced neighbor designs are constructed for v even. In class I, v/2 of all unordered pairs of two distinct treatments appear twice as neighbors while the remaining ones appear once. In class II, 3v/2 of all unordered pairs appear twice as neighbors.
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- Noreen, K., et al.
(author)
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Some new constructions of minimal efficient circular nearly strongly balanced neighbor designs
- 2023
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In: Journal of King Saud University - Science. - : Elsevier. - 1018-3647. ; 35:6
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Journal article (peer-reviewed)abstract
- Neighbor designs are popular to control neighbor effects. Among neighbor designs, strongly balanced neighbor designs are important to estimate treatment effects and neighbor effects independently. Minimal circular strongly balanced neighbor designs (MCSBNDs) can be obtained only for odd v (number of treatments). For v even, minimal circular nearly strongly balanced neighbor designs are used which satisfied all conditions of MCSBNDs except that the treatment labeled as (v − 1) does not appear as its own neighbor. These designs can be converted directly in some other useful classes of neighbor designs. These designs are efficient to minimize the bias due to the neighbor effects.
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- Steadman, Randolph H., et al.
(author)
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Screen-Based Simulation for Training and Automated Assessment of Teamwork Skills Comparing 2 Modes With Different Interactivity
- 2021
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In: Simulation in Healthcare. - : LIPPINCOTT WILLIAMS & WILKINS. - 1559-2332 .- 1559-713X. ; 16:5, s. 318-326
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Journal article (peer-reviewed)abstract
- Introduction: The need for teamwork training is well documented; however, teaching these skills is challenging given the logistics of assembling individual team members together to train in person. We designed 2 modes of screen-based simulation for training teamwork skills to assess whether interactivity with nonplayer characters was necessary for in-game performance gains or for player satisfaction with the experience. Methods: Mixed, randomized, repeated measures study with licensed healthcare providers block-stratified and randomized to evaluation-participant observes and evaluates the team player in 3 scenarios-and game play-participant is immersed as the leader in the same 3 scenarios. Teamwork construct scores (leadership, communication, situation monitoring, mutual support) from an ontology-based, Bayesian network assessment model were analyzed using mixed randomized repeated measures analyses of variance to compare performance, across scenarios and modes. Learning was measured by pretest and posttest quiz scores. User experience was evaluated using chi(2) analyses. Results: Among 166 recruited and randomized participants, 120 enrolled in the study and 109 had complete data for analysis. Mean composite teamwork Bayesian network scores improved for successive scenarios in both modes, with evaluation scores statistically higher than game play for every teamwork construct and scenario (r = 0.73, P = 0.000). Quiz scores improved from pretest to posttest (P = 0.004), but differences between modes were not significant. Conclusions: For training teamwork skills using screen-based simulation, interactivity of the player with the nonplayer characters is not necessary for in-game performance gains or for player satisfaction with the experience.
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