| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
- Elding, Lars Ivar, et al.
(författare)
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Detection of a Novel Intermediate in the Addition of Thiols to Osmium Carbonyl Clusters
- 1998
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Ingår i: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1364-548X .- 1359-7345. ; 1998:24, s. 2721-2722
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Tidskriftsartikel (refereegranskat)abstract
- Spectroscopic studies of the reaction of [Os-3(CO)(11)MeCN)] with para-thiocresol to form [Os-3(mu-H)(CO)(10)(mu-SC6H4Me-p)] indicate that the reaction proceeds via a two-step consecutive process involving the intermediate [Os-3(CO)(11)-(MeC6H4SH-p)], in which there is an agostic Os-H-S interaction.
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| 3. |
- Swift, Imogen J, et al.
(författare)
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A systematic review of progranulin concentrations in biofluids in over 7,000 people-assessing the pathogenicity of GRN mutations and other influencing factors.
- 2024
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Ingår i: Alzheimer's Research & Therapy. - 1758-9193. ; 16:1
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Tidskriftsartikel (refereegranskat)abstract
- Pathogenic heterozygous mutations in the progranulin gene (GRN) are a key cause of frontotemporal dementia (FTD), leading to significantly reduced biofluid concentrations of the progranulin protein (PGRN). This has led to a number of ongoing therapeutic trials aiming to treat this form of FTD by increasing PGRN levels in mutation carriers. However, we currently lack a complete understanding of factors that affect PGRN levels and potential variation in measurement methods. Here, we aimed to address this gap in knowledge by systematically reviewing published literature on biofluid PGRN concentrations.Published data including biofluid PGRN concentration, age, sex, diagnosis and GRN mutation were collected for 7071 individuals from 75 publications. The majority of analyses (72%) had focused on plasma PGRN concentrations, with many of these (56%) measured with a single assay type (Adipogen) and so the influence of mutation type, age at onset, sex, and diagnosis were investigated in this subset of the data.We established a plasma PGRN concentration cut-off between pathogenic mutation carriers and non-carriers of 74.8ng/mL using the Adipogen assay based on 3301 individuals, with a CSF concentration cut-off of 3.43ng/mL. Plasma PGRN concentration varied by GRN mutation type as well as by clinical diagnosis in those without a GRN mutation. Plasma PGRN concentration was significantly higher in women than men in GRN mutation carriers (p=0.007) with a trend in non-carriers (p=0.062), and there was a significant but weak positive correlation with age in both GRN mutation carriers and non-carriers. No significant association was seen with weight or with TMEM106B rs1990622 genotype. However, higher plasma PGRN levels were seen in those with the GRN rs5848 CC genotype in both GRN mutation carriers and non-carriers.These results further support the usefulness of PGRN concentration for the identification of the large majority of pathogenic mutations in the GRN gene. Furthermore, these results highlight the importance of considering additional factors, such as mutation type, sex and age when interpreting PGRN concentrations. This will be particularly important as we enter the era of trials for progranulin-associated FTD.
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| 4. |
- Esteve-Codina, Anna, et al.
(författare)
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Gender specific airway gene expression in COPD sub-phenotypes supports a role of mitochondria and of different types of leukocytes
- 2021
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Chronic obstructive pulmonary disease (COPD) is a destructive inflammatory disease and the genes expressed within the lung are crucial to its pathophysiology. We have determined the RNAseq transcriptome of bronchial brush cells from 312 stringently defined ex-smoker patients. Compared to healthy controls there were for males 40 differentially expressed genes (DEGs) and 73 DEGs for females with only 26 genes shared. The gene ontology (GO) term "response to bacterium" was shared, with several different DEGs contributing in males and females. Strongly upregulated genes TCN1 and CYP1B1 were unique to males and females, respectively. For male emphysema (E)-dominant and airway disease (A)-dominant COPD (defined by computed tomography) the term "response to stress" was found for both sub-phenotypes, but this included distinct up-regulated genes for the E-sub-phenotype (neutrophil-related CSF3R, CXCL1, MNDA) and for the A-sub-phenotype (macrophage-related KLF4, F3, CD36). In E-dominant disease, a cluster of mitochondria-encoded (MT) genes forms a signature, able to identify patients with emphysema features in a confirmation cohort. The MT-CO2 gene is upregulated transcriptionally in bronchial epithelial cells with the copy number essentially unchanged. Both MT-CO2 and the neutrophil chemoattractant CXCL1 are induced by reactive oxygen in bronchial epithelial cells. Of the female DEGs unique for E- and A-dominant COPD, 88% were detected in females only. In E-dominant disease we found a pronounced expression of mast cell-associated DEGs TPSB2, TPSAB1 and CPA3. The differential genes discovered in this study point towards involvement of different types of leukocytes in the E- and A-dominant COPD sub-phenotypes in males and females.
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| 5. |
- George, Leena, et al.
(författare)
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Blood eosinophil count and airway epithelial transcriptome relationships in COPD versus asthma
- 2020
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Ingår i: Allergy. European Journal of Allergy and Clinical Immunology. - : WILEY. - 0105-4538 .- 1398-9995. ; 75:2, s. 370-380
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Tidskriftsartikel (refereegranskat)abstract
- Background: Whether the clinical or pathophysiologic significance of the "treatable trait" high blood eosinophil count in COPD is the same as for asthma remains controversial. We sought to determine the relationship between the blood eosinophil count, clinical characteristics and gene expression from bronchial brushings in COPD and asthma.Methods: Subjects were recruited into a COPD (emphysema versus airway disease [EvA]) or asthma cohort (Unbiased BIOmarkers in PREDiction of respiratory disease outcomes, U-BIOPRED). We determined gene expression using RNAseq in EvA (n = 283) and Affymetrix microarrays in U-BIOPRED (n = 85). We ran linear regression analysis of the bronchial brushings transcriptional signal versus blood eosinophil counts as well as differential expression using a blood eosinophil > 200 cells/mu L as a cut-off. The false discovery rate was controlled at 1% (with continuous values) and 5% (with dichotomized values).Results: There were no differences in age, gender, lung function, exercise capacity and quantitative computed tomography between eosinophilic versus noneosinophilic COPD cases. Total serum IgE was increased in eosinophilic asthma and COPD. In EvA, there were 12 genes with a statistically significant positive association with the linear blood eosinophil count, whereas in U-BIOPRED, 1197 genes showed significant associations (266 positive and 931 negative). The transcriptome showed little overlap between genes and pathways associated with blood eosinophil counts in asthma versus COPD. Only CST1 was common to eosinophilic asthma and COPD and was replicated in independent cohorts.Conclusion: Despite shared "treatable traits" between asthma and COPD, the molecular mechanisms underlying these clinical entities are predominately different.
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| 8. |
- Larsson, Lars, 1983-, et al.
(författare)
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Adaptive and Application-agnostic Caching in Service Meshes for Resilient Cloud Applications
- 2021
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Ingår i: Proceedings of the 2021 IEEE Conference on Network Softwarization (NetSoft) : Accelerating Network Softwarization in the Cognitive Age - Accelerating Network Softwarization in the Cognitive Age. - : IEEE. - 9781665405225 ; , s. 176-180
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Konferensbidrag (refereegranskat)abstract
- Service meshes factor out code dealing with inter-micro-service communication. The overall resilience of a cloud application is improved if constituent micro-services return stale data, instead of no data at all. This paper proposes and implements application agnostic caching for micro services. While caching is widely employed for serving web service traffic, its usage in inter-micro-service communication is lacking. Micro-services responses are highly dynamic, which requires carefully choosing adaptive time-to-life caching algorithms. Our approach is application agnostic, is cloud native, and supports gRPC. We evaluate our approach and implementation using the micro-service benchmark by Google Cloud called Hipster Shop. Our approach results in caching of about 80% of requests. Results show the feasibility and efficiency of our approach, which encourages implementing caching in service meshes. Additionally, we make the code, experiments, and data publicly available.
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| 9. |
- Mendonca, Luciana De Michelis, et al.
(författare)
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Sports injury prevention programmes from the sports physical therapists perspective: An international expert Delphi approach
- 2022
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Ingår i: Physical Therapy in Sport. - Oxford, United Kingdom : Elsevier. - 1466-853X .- 1873-1600. ; 55, s. 146-154
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To provide consensus on how to plan, organize and implement exercise-based injury prevention program (IPP) in sports.Design: Delphi.Setting: LimeSurvey platform.Participants: Experienced sports physical therapists from the International Federation of Sports Physical Therapy member countries.Main outcome measures: Factors related to sports IPP planning, organization and implementation.Results: We included 305 participants from 32 countries. IPP planning should be based on an athletes injury history, on pre-season screening results, and on injury rates (respectively, 98%, 92%, 89% agreement). In total 97% participants agreed that IPP organization should depend on the athletes age, 93% on the competition level, and 93% on the availability of low-cost materials. It was agreed that IPP should mainly be implemented in warm-up sessions delivered by the head or strength/conditioning coach, with physical training sessions and individual physical therapy sessions (respectively, 94%, 92%, 90% agreement).Conclusion: Strong consensus was reached on (1) IPP based on the athletes injury history, pre-season screening and evidence-based sports-specific injury rates; (2) IPP organization based on the athletes age, competition level, and the availability of low-cost materials and (3) IPP implementation focussing on warm-up sessions implemented by the strength/conditioning coach, and/or individual prevention sessions by the physical therapist.
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