| 1. |
- Wortman, J. R., et al.
(författare)
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The 2008 update of the Aspergillus nidulans genome annotation: A community effort
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46, s. S2-S13
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Tidskriftsartikel (refereegranskat)abstract
- The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology. (C) 2009 Elsevier Inc. All rights reserved.
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| 2. |
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| 3. |
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| 4. |
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| 5. |
- Baron, J. S., et al.
(författare)
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Synthesis Centers as Critical Research Infrastructure
- 2017
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Ingår i: Bioscience. - : Oxford University Press (OUP). - 0006-3568 .- 1525-3244. ; 67:8, s. 750-759
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Tidskriftsartikel (refereegranskat)abstract
- Synthesis centers offer a unique amalgam of culture, infrastructure, leadership, and support that facilitates creative discovery on issues crucial to science and society. The combination of logistical support, postdoctoral or senior fellowships, complex data management, informatics and computing capability or expertise, and most of all, opportunity for group discussion and reflection lowers the "activation energy" necessary to promote creativity and the cross-fertilization of ideas. Synthesis centers are explicitly created and operated as community-oriented infrastructure, with scholarly directions driven by the ever-changing interests and needs of an open and inclusive scientific community. The last decade has seen a rise in the number of synthesis centers globally but also the end of core federal funding for several, challenging the sustainability of the infrastructure for this key research strategy. Here, we present the history and rationale for supporting synthesis centers, integrate insights arising from two decades of experience, and explore the challenges and opportunities for long-term sustainability.
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| 6. |
- Christensen, P S, et al.
(författare)
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Environmental cadmium and lead exposure and anti-Müllerian hormone in pregnant women
- 2016
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Ingår i: Reproductive Toxicology. - : Elsevier BV. - 1873-1708 .- 0890-6238. ; 61, s. 114-119
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Anti-Müllerian Hormone (AMH) has been suggested as a marker for ovarian function. Cadmium and lead have been suggested to reduce female fecundity. In this study we aimed to investigate whether environmental exposure to cadmium and lead was associated with alterations in serum-AMH.MATERIALS AND METHOD: The associations between serum-AMH and whole blood cadmium or lead were investigated by general linear models in a population-based sample of 117 pregnant women.RESULTS: The mean concentrations of blood cadmium and lead were 0.71μg/L and 17.4μg/L, respectively. The mean serum-AMH was 17.3pmol/L. No association between lead and AMH was detected. In the cadmium analysis the adjusted mean AMH level (95% CI) in the highest exposure tertile was 12.4 (6.4;23.8) compared to 5.6 (2.7;11.4) in the lowest exposure tertile (p=0.06).CONCLUSION: The study provides suggestive evidence that environmental exposure to cadmium, but not lead, may alter the level of AMH.
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| 7. |
- Ek, M., et al.
(författare)
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Probing Catalyst Surfaces at the Atomic-scale
- 2023
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Ingår i: Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. - 1435-8115. ; 29:1, s. 1291-1291
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Tidskriftsartikel (refereegranskat)
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| 8. |
- Lastras-Martínez, L. F., et al.
(författare)
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Reflectance difference spectroscopy of GaAs asymmetric surface quantum wells above the fundamental gap
- 1998
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Ingår i: Physica status solidi. A, Applied research. - 0031-8965 .- 1521-396X. ; 170:2, s. 317-321
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Tidskriftsartikel (refereegranskat)abstract
- We report Reflectance Difference (RD) measurement on (001) GaAs surface quantum wells (QW) under Ultra High Vacuum (UHV) conditions from 1.7 to 5.0eV. The QW is embedded between an arsenic-rich reconstructed GaAs surface and an AlAs barrier. The samples, grown by MBE with a protective arsenic cap layer, were heated to 320 and 430°C to desorb the As layer and form c(4 x 4) and (2 x 4) surface reconstructions, respectively. By modifying the surface reconstructure, we are able to separate the contributions to the optical anisotropy from the surface region (mainly associated with the As dimers) from those originating below the surface.
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| 9. |
- Baumgartner, D, et al.
(författare)
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OralDisk: A Chair-Side Compatible Molecular Platform Using Whole Saliva for Monitoring Oral Health at the Dental Practice
- 2021
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Ingår i: Biosensors. - : MDPI AG. - 2079-6374. ; 11:11
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Tidskriftsartikel (refereegranskat)abstract
- Periodontitis and dental caries are two major bacterially induced, non-communicable diseases that cause the deterioration of oral health, with implications in patients’ general health. Early, precise diagnosis and personalized monitoring are essential for the efficient prevention and management of these diseases. Here, we present a disk-shaped microfluidic platform (OralDisk) compatible with chair-side use that enables analysis of non-invasively collected whole saliva samples and molecular-based detection of ten bacteria: seven periodontitis-associated (Aggregatibacter actinomycetemcomitans, Campylobacter rectus, Fusobacterium nucleatum, Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola) and three caries-associated (oral Lactobacilli, Streptococcus mutans, Streptococcus sobrinus). Each OralDisk test required 400 µL of homogenized whole saliva. The automated workflow included bacterial DNA extraction, purification and hydrolysis probe real-time PCR detection of the target pathogens. All reagents were pre-stored within the disk and sample-to-answer processing took < 3 h using a compact, customized processing device. A technical feasibility study (25 OralDisks) was conducted using samples from healthy, periodontitis and caries patients. The comparison of the OralDisk with a lab-based reference method revealed a ~90% agreement amongst targets detected as positive and negative. This shows the OralDisk’s potential and suitability for inclusion in larger prospective implementation studies in dental care settings.
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| 10. |
- Deans, Andrew R, et al.
(författare)
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Finding Our Way through Phenotypes.
- 2015
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Ingår i: PLoS Biology. - : Public Library of Science (PLoS). - 1545-7885. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.
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| 11. |
- Forner, L. E., et al.
(författare)
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Hyperbaric oxygen treatment of mandibular osteoradionecrosis: Combined data from the two randomized clinical trials DAHANCA-21 and NWHHT2009-1
- 2022
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Ingår i: Radiotherapy and Oncology. - : Elsevier BV. - 0167-8140. ; 166, s. 137-144
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Osteoradionecrosis (ORN) of the mandible is a serious complication of head and neck radiotherapy. This study aims to investigate the effect of hyperbaric oxygen (HBO) treatment on ORN in two randomized, controlled multicentre trials. Methods and materials: Patients with ORN with indication for surgical treatment were randomised to either group 1: surgical removal of necrotic mandibular bone supplemented by 30 pre- and 10 postoperative HBO exposures at 243 kPa for 90 min each, or group 2: surgical removal of necrotic bone only. Primary outcome was healing of ORN one year after surgery evaluated by a clinically adjusted version of the Common Toxicity Criteria of Adverse Events (CTCAE) v 3.0. Secondary outcomes included xerostomia, unstimulated and stimulated whole salivation rates, trismus, dysphagia, pain, Activities of Daily Living (ADL) and quality of life according to EORTC. Data were combined from two separate trials. Ninety-seven were enrolled and 65 were eligible for the intent-to-treat analysis. The 33% drop-out was equally distributed between groups. Results: In group 1, 70% (21/30) healed compared to 51% (18/35) in group 2. HBO was associated with an increased chance of healing independent of baseline ORN grade or smoking status as well as improved xerostomia, unstimulated whole salivary flow rate, and dysphagia. Due to insufficient recruitment, none of the endpoints reached a statistically significant difference between groups. ADL data could only be obtained from 50 patients. Conclusion: Hyperbaric oxygen did not significantly improve the healing outcome of osteoradionecrosis after surgical removal of necrotic bone as compared to standard care (70% vs. 51%). This effect is not statistically significant due to the fact that the study was underpowered and is therefore prone to type II error. © 2021 The Authors
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| 12. |
- Iles, W. J. D., et al.
(författare)
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The phylogeny of Heliconia (Heliconiaceae) and the evolution of floral presentation
- 2017
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 117, s. 150-167
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Tidskriftsartikel (refereegranskat)abstract
- Heliconia (Heliconiaceae, order Zingiberales) is among the showiest plants of the Neotropical rainforest and represent a spectacular co-evolutionary radiation with hummingbirds. Despite the attractiveness and ecological importance of many Heliconia, the genus has been the subject of limited molecular phylogenetic studies. We sample seven markers from the plastid and nuclear genomes for 202 samples of Heliconia. This represents ca. 75% of accepted species and includes coverage of all taxonomic subgenera and sections. We date this phylogeny using fossils associated with other families in the Zingiberales; in particular we review and evaluate the Eocene fossil Ensete oregonense. We use this dated phylogenetic framework to evaluate the evolution of two components of flower orientation that are hypothesized to be important for modulating pollinator discrimination and pollen placement: resupination and erect versus pendant inflorescence habit. Our phylogenetic results suggest that the monophyletic Melanesian sub-genus Heliconiopsis and a small Glade of Ecuadorian species are together the sister group to the rest of Heliconia. Extant diversity of Heliconia originated in the Late Eocene (39 Ma) with rapid diversification through the Early Miocene, making it the oldest known Glade of hummingbird-pollinated plants. Most described subgenera and sections are not monophyletic, though closely related groups of species, often defined by shared geography, mirror earlier morphological cladistic analyses. Evaluation of changes in resupination and inflorescence habit suggests that these characters are more homoplasious than expected, and this largely explains the non-monophyly of previously circumscribed subgenera, which were based on these characters. We also find strong evidence for the correlated evolution of resupination and inflorescence habit. The correlated model suggests that the most recent common ancestor of all extant Heliconia had resupinate flowers and erect inflorescences. Finally, we note our nearly complete species sampling and dated phylogeny allow for an assessment of taxonomic history in terms of phylogenetic diversity. We find approximately half of the currently recognized species, corresponding to half of the phylogenetic diversity, have been described since 1975, highlighting the continued importance of basic taxonomic research and conservation initiatives to preserve both described and undiscovered species of Heliconia. (C) 2016 Elsevier Inc. All rights reserved.
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| 13. |
- Loures, Flávio V, et al.
(författare)
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Recognition of Aspergillus fumigatus Hyphae by Human Plasmacytoid Dendritic Cells Is Mediated by Dectin-2 and Results in Formation of Extracellular Traps
- 2015
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Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 11:2
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Tidskriftsartikel (refereegranskat)abstract
- Plasmacytoid dendritic cells (pDCs) were initially considered as critical for innate immunity to viruses. However, our group has shown that pDCs bind to and inhibit the growth of Aspergillus fumigatus hyphae and that depletion of pDCs renders mice hypersusceptible to experimental aspergillosis. In this study, we examined pDC receptors contributing to hyphal recognition and downstream events in pDCs stimulated by A. fumigatus hyphae. Our data show that Dectin-2, but not Dectin-1, participates in A. fumigatus hyphal recognition, TNF-α and IFN-α release, and antifungal activity. Moreover, Dectin-2 acts in cooperation with the FcRγ chain to trigger signaling responses. In addition, using confocal and electron microscopy we demonstrated that the interaction between pDCs and A. fumigatus induced the formation of pDC extracellular traps (pETs) containing DNA and citrullinated histone H3. These structures closely resembled those of neutrophil extracellular traps (NETs). The microarray analysis of the pDC transcriptome upon A. fumigatus infection also demonstrated up-regulated expression of genes associated with apoptosis as well as type I interferon-induced genes. Thus, human pDCs directly recognize A. fumigatus hyphae via Dectin-2; this interaction results in cytokine release and antifungal activity. Moreover, hyphal stimulation of pDCs triggers a distinct pattern of pDC gene expression and leads to pET formation.
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| 14. |
- Maher, Ann Butler, et al.
(författare)
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Acute nursing care of the older adult with fragility hip fracture : An international perspective (Part 2)
- 2013
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Ingår i: International Journal of Orthopaedic and Trauma Nursing. - : Elsevier. - 1878-1241 .- 1878-1292. ; 17:1, s. 4-18
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Tidskriftsartikel (refereegranskat)abstract
- The second part of this paper provides those who care for orthopaedic patients with evidence-supported international perspectives about acute nursing care of the older adult with fragility hip fracture. Developed by an international group of nurse experts and guided by a range of information from research and clinical practice, it focuses on nurse sensitive quality indicators during the acute hospitalisation for fragility hip fracture. Optimal care for the patient who has experienced such a fracture is the focus. This includes (in the first, earlier, part):PainDeliriumand in this partPressure UlcersFluid Balance/NutritionConstipation/Catheter Associated Urinary Tract InfectionVigilant nursing assessment and prompt intervention may prevent the development of the complications we discuss. If they do occur and are identified early on, they may resolve with appropriate and timely nursing management.This “tool kit” has been developed under the auspices of the International Collaboration of Orthopaedic Nursing (ICON) a coalition of national associations of orthopaedic nursing (www.orthopaedicnursing.org).
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| 15. |
- Maher, Ann Butler, et al.
(författare)
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Acute nursing care of the older adult with fragility hip fracture : An international perspective (Part 1)
- 2012
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Ingår i: International Journal of Orthopaedic and Trauma Nursing. - : Elsevier. - 1878-1241 .- 1878-1292. ; 16:4, s. 177-194
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Tidskriftsartikel (refereegranskat)abstract
- This paper provides those who care for orthopaedic patients with evidence-supported international perspectives about acute nursing care of the older adult with fragility hip fracture. Developed by an international group of nurse experts and guided by a range of information from research and clinical practice, it focuses on nurse sensitive quality indicators during the acute hospitalisation for fragility hip fracture. Optimal care for the patient who has experienced such a fracture is the focus here. This includes in this part:PainDeliriumand in the second, subsequent, partPressure UlcersFluid Balance/NutritionConstipation/Catheter Associated Urinary Tract InfectionVigilant nursing assessment and prompt intervention may prevent the development of the complications we discuss. If they do occur and are identified early on, they may resolve with appropriate and timely nursing management.This “tool kit” has been developed under the auspices of the International Collaboration of Orthopaedic Nursing (ICON) a coalition of national associations of orthopaedic nursing (www.orthopaedicnursing.org).Previous article in issue
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| 16. |
- Moczek, Armin P., et al.
(författare)
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The significance and scope of evolutionary developmental biology : a vision for the 21st century
- 2015
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Ingår i: Evolution & development. ; 17:3, s. 198-219
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Tidskriftsartikel (refereegranskat)abstract
- Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century.
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