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| 3. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 6. |
- Öling, S., et al.
(författare)
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A human stomach cell type transcriptome atlas
- 2024
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Ingår i: BMC Biology. - : Springer Nature. - 1741-7007. ; 22:1
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Tidskriftsartikel (refereegranskat)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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| 7. |
- Angelo, Kristina M., et al.
(författare)
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Zika among international travellers presenting to GeoSentinel sites, 2012-2019 : implications for clinical practice
- 2020
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Ingår i: Journal of Travel Medicine. - : Oxford University Press. - 1195-1982 .- 1708-8305. ; 27:4
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Tidskriftsartikel (refereegranskat)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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| 8. |
- Bucar, Franz, et al.
(författare)
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Amentoflavone from Biophytum sensitivum and its effect on COX-1/COX-2 catalysed prostaglandin biosynthesis
- 1998
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Ingår i: Planta Medica. - : Thieme. - 0032-0943 .- 1439-0221. ; 64:4, s. 373-374
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Tidskriftsartikel (refereegranskat)abstract
- Amentoflavone (13′, ll8-biapigenin) was isolated from the roots of Biophytum sensitivum DC. (Oxalidaceae) and proved to be a selective inhibitor of cyclooxygenase (COX)-1 catalysed prostaglandin biosynthesis when tested in vitro with an IC50 value of 12.4 µM (standard: indomethacin, IC50 = 1.1 µM). Doses of up to 37 µM showed only a slight inhibition in the corresponding COX-2 assay. Quantification of amentoflavone was carried out by reversed phase HPLC in methanolic and aqueous extracts of the roots, stems and leaves. Highest amounts of amentoflavone were detected in methanolic extracts of roots and stems (0.26-0.35%), while considerably lower amounts were detected in the corresponding water extracts.
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| 9. |
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| 10. |
- Hamer, Davidson H., et al.
(författare)
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Travel-Associated Zika Virus Disease Acquired in the Americas Through February 2016 A GeoSentinel Analysis
- 2017
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Ingår i: Annals of Internal Medicine. - Philadelphia : American College of Physicians. - 0003-4819 .- 1539-3704. ; 166:2, s. 99-108
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Tidskriftsartikel (refereegranskat)abstract
- Background: Zika virus has spread rapidly in the Americas and has been imported into many nonendemic countries by travelers. Objective: To describe clinical manifestations and epidemiology of Zika virus disease in travelers exposed in the Americas. Design: Descriptive, using GeoSentinel records. Setting: 63 travel and tropical medicine clinics in 30 countries. Patients: Ill returned travelers with a confirmed, probable, or clinically suspected diagnosis of Zika virus disease seen between January 2013 and 29 February 2016. Measurements: Frequencies of demographic, trip, and clinical characteristics and complications. Results: Starting in May 2015, 93 cases of Zika virus disease were reported. Common symptoms included exanthema (88%), fever (76%), and arthralgia (72%). Fifty-nine percent of patients were exposed in South America; 71% were diagnosed in Europe. Case status was established most commonly by polymerase chain reaction (PCR) testing of blood and less often by PCR testing of other body fluids or serology and plaque-reduction neutralization testing. Two patients developed Guillain-Barre syndrome, and 3 of 4 pregnancies had adverse outcomes (microcephaly, major fetal neurologic abnormalities, and intrauterine fetal death). Limitation: Surveillance data collected by specialized clinics may not be representative of all ill returned travelers, and denominator data are unavailable. Conclusion: These surveillance data help characterize the clinical manifestations and adverse outcomes of Zika virus disease among travelers infected in the Americas and show a need for global standardization of diagnostic testing. The serious fetal complications observed in this study highlight the importance of travel advisories and prevention measures for pregnant women and their partners. Travelers are sentinels for global Zika virus circulation and may facilitate further transmission.
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| 11. |
- Hassan, Jamshaidul, et al.
(författare)
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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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Ingår i: Communications in Statistics - Theory and Methods. - : Informa UK Limited. - 0361-0926 .- 1532-415X. ; 52:16, s. 5587-5605
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Tidskriftsartikel (refereegranskat)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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| 14. |
- Huaraca Huasco, Walter, et al.
(författare)
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Fine root dynamics across pantropical rainforest ecosystems
- 2021
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Ingår i: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 27:15, s. 3657-3680
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Tidskriftsartikel (refereegranskat)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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| 15. |
- Nadeem, Muhammad, et al.
(författare)
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New generators for minimal circular generalised neighbour designs in blocks of two different sizes
- 2023
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Ingår i: Statistics in Transition New Series. - 1234-7655 .- 2450-0291. ; 24:2, s. 85-92
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Tidskriftsartikel (refereegranskat)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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| 16. |
- Nilsson, Gisela M A, 1973, et al.
(författare)
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Loss of E-cadherin expression is not a prerequisite for c-erbB2-induced epithelial-mesenchymal transition.
- 2014
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Ingår i: International journal of oncology. - : Spandidos Publications. - 1791-2423 .- 1019-6439. ; 45:1, s. 82-94
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Tidskriftsartikel (refereegranskat)abstract
- Recent research into the mechanisms of tumour cell invasiveness has highlighted the parallels between carcinogenesis and epithelial-mesenchymal transition (EMT), originally described as a developmental transdifferentiation program but also implicated in fibrosis and cancer. In a model system for mammary carcinogenesis, we previously observed that induced signalling from a homodimer of the c-erbB2 (HER2) receptor tyrosine kinase in an initially non-malignant mammary cell line caused EMT where i)cell scattering occurred before downregulation of the cell-cell adhesion molecule E-cadherin and ii)the progress of EMT was dramatically delayed when cells were grown at high density. Here, we have further analysed these phenomena. Ectopic expression of E-cadherin concomitant with c-erbB2 signalling was unable to impede the progression of EMT, suggesting that E-cadherin downregulation is not required for EMT. Furthermore, fibroblast-like cells isolated after EMT induced in the presence or absence of ectopic E-cadherin expression showed highly similar morphology and vimentin expression. E-cadherin expressed in these fibroblastic cells had a subcellular localisation similar to that found in epithelial cells, but it exhibited a much weaker attachment to the cytoskeleton, suggesting cytoskeletal rearrangements as an important mechanism in EMT-associated cell scattering. We also investigated whether density-dependent inhibition of EMT is mediated by E-cadherin as a sensor for cell-cell contact, by expressing dominant-negative E-cadherin. While expression of this mutant weakened cell-cell adhesion, it failed to facilitate EMT at high cell densities. These results indicate that loss of E-cadherin expression is a consequence rather than a cause of c-erbB2-induced EMT and that density‑dependent inhibition of EMT is not mediated by E-cadherin signalling.
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| 17. |
- Noreen, Erik, et al.
(författare)
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Hotbildspolitikens konsekvenser
- 2001
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Ingår i: Hotbildernas politik. - : Stockholm: Utrikespolitiska institutet. ; , s. 99-110
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 18. |
- Noreen, Khadija, et al.
(författare)
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Some important classes of non-directional minimal circular weakly balanced neighbor designs
- 2023
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Ingår i: Communications in statistics. Simulation and computation. - 0361-0918 .- 1532-4141. ; , s. 1-10
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Tidskriftsartikel (refereegranskat)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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| 19. |
- Noreen, K., et al.
(författare)
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Some new constructions of minimal efficient circular nearly strongly balanced neighbor designs
- 2023
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Ingår i: Journal of King Saud University - Science. - : Elsevier. - 1018-3647. ; 35:6
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Tidskriftsartikel (refereegranskat)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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| 20. |
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| 21. |
- Steadman, Randolph H., et al.
(författare)
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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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Ingår i: Simulation in Healthcare. - : LIPPINCOTT WILLIAMS & WILKINS. - 1559-2332 .- 1559-713X. ; 16:5, s. 318-326
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Tidskriftsartikel (refereegranskat)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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| 22. |
- van der Post, Sjoerd, 1981, et al.
(författare)
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Structural weakening of the colonic mucus barrier is an early event in ulcerative colitis pathogenesis
- 2019
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Ingår i: Gut. - : BMJ. - 0017-5749 .- 1468-3288. ; 68:12, s. 2142-2151
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Tidskriftsartikel (refereegranskat)abstract
- Objective The colonic inner mucus layer protects us from pathogens and commensal-induced inflammation, and has been shown to be defective in active UC. The aim of this study was to determine the underlying compositional alterations, their molecular background and potential contribution to UC pathogenesis. Design In this single-centre case-control study, sigmoid colon biopsies were obtained from patients with UC with ongoing inflammation (n=36) or in remission (n=28), and from 47 patients without colonic disease. Mucus samples were collected from biopsies ex vivo, and their protein composition analysed by nanoliquid chromatography-tandem mass spectrometry. Mucus penetrability and goblet cell responses to microbial stimulus were assessed in a subset of patients. Results The core mucus proteome was found to consist of a small set of 29 secreted/transmembrane proteins. In active UC, major structural mucus components including the mucin MUC2 (p<0.0001) were reduced, also in non-inflamed segments. Active UC was associated with decreased numbers of sentinel goblet cells and attenuation of the goblet cell secretory response to microbial challenge. Abnormal penetrability of the inner mucus layer was observed in a subset of patients with UC (12/40; 30%). Proteomic alterations in penetrable mucus samples included a reduction of the SLC26A3 apical membrane anion exchanger, which supplies bicarbonate required for colonic mucin barrier formation. Conclusion Core mucus structural components were reduced in active UC. These alterations were associated with attenuation of the goblet cell secretory response to microbial challenge, but occurred independent of local inflammation. Thus, mucus abnormalities are likely to contribute to UC pathogenesis.
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