| 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. |
- Allanach, Benjamin C., et al.
(författare)
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Simple and statistically sound strategies for analysing physical theories
- 2022
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Ingår i: Reports on progress in physics (Print). - : Institute of Physics Publishing (IOPP). - 0034-4885 .- 1361-6633. ; 85:5
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Forskningsöversikt (refereegranskat)abstract
- Physical theories that depend on many parameters or are tested against data from many different experiments pose unique challenges to statistical inference. Many models in particle physics, astrophysics and cosmology fall into one or both of these categories. These issues are often sidestepped with statistically unsound ad hoc methods, involving intersection of parameter intervals estimated by multiple experiments, and random or grid sampling of model parameters. Whilst these methods are easy to apply, they exhibit pathologies even in low-dimensional parameter spaces, and quickly become problematic to use and interpret in higher dimensions. In this article we give clear guidance for going beyond these procedures, suggesting where possible simple methods for performing statistically sound inference, and recommendations of readily-available software tools and standards that can assist in doing so. Our aim is to provide any physicists lacking comprehensive statistical training with recommendations for reaching correct scientific conclusions, with only a modest increase in analysis burden. Our examples can be reproduced with the code publicly available at Zenodo.
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| 3. |
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| 4. |
- Aziz, Emad F., et al.
(författare)
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Photoinduced formation of N-2 molecules in ammonium compounds
- 2007
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 111:39, s. 9662-9669
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Tidskriftsartikel (refereegranskat)abstract
- Via fluorescence yield (FY) and resonant inelastic scattering spectroscopy in the soft X-ray range we find that soft X-rays induce formation of N-2 molecules in solid NH4Cl and in related compounds. The nitrogen molecules form weak bonds in NH4Cl, so that a substantial fraction of the molecules remains in the sample. From measurements of the FY as a function of exposure and temperature, the rates for the photochemical processes are estimated. At elevated temperatures (363 K), several nitrogen atoms are removed from the sample per incoming photon. At lower temperatures (233 K), the rate is reduced to around 0.02 nitrogen atoms for each incoming photon. Virtually all these atoms form N-2 molecules which are bound in the sample. The generality and implications of these results are briefly discussed.
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| 5. |
- C Kapetanovic, Meliha, et al.
(författare)
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Development of functional impairment and disability in rheumatoid arthritis patients followed for 20 years - relation to disease activity, joint damage and comorbidity.
- 2015
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Ingår i: Arthritis Care and Research. - : Wiley. - 2151-4658 .- 2151-464X. ; 67:3, s. 340-348
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Tidskriftsartikel (refereegranskat)abstract
- Objectives. To study the course of impairment measured by signals of functional impairment (SOFI) and disability measured by health assessment questionnaire (HAQ) over 20 years in rheumatoid arthritis (RA) patients followed from diagnosis. To explore the contribution of disease activity, joint damage and comorbidity to variation of SOFI and HAQ over time. Methods. RA patients diagnosed 1985-1989 were prospectively monitored. There were 183 patients, 63 % were women, mean (SD) age was 52 (12) years. Disease activity was measured by 44-joint DAS, joint damage by Larsen score and comorbidity by Charlson Comorbidity Index. Contribution of comorbidity, DAS and joint damage on development of SOFI and HAQ was studied at 0,5,10, 15 and 20 years follow up (hierarchical regression model) and over the total study period using (longitudinal regression model). Results. SOFI progressed over 20 years while progression of HAQ levelled off after 10 years. For SOFI, DAS and joint damage contributed the most (2-28 % and 3-31%, respectively). Over 20 years, SOFI was explained by DAS (20%), joint damage (20%), age (7%) and comorbidity (4%). For HAQ, DAS contributed the most (4-24%). Over 20 years, HAQ was explained by DAS (20%), joint damage (2%), gender (7%), comorbidity (6%) and age (4%). Conclusion. Over 20 years, 51% of the variation of SOFI and 39% of the variation of HAQ could be explained by age, gender and variations in comorbidity, disease activity and joint damage. Over time, disease activity contributed significantly to both SOFI and HAQ. Joint damage contributed predominantly to SOFI. © 2014 American College of Rheumatology.
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| 6. |
- Eberhardt, Mirjam, et al.
(författare)
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H2S and NO cooperatively regulate vascular tone by activating a neuroendocrine HNO-TRPA1-CGRP signalling pathway.
- 2014
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5:Jul 15
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Tidskriftsartikel (refereegranskat)abstract
- Nitroxyl (HNO) is a redox sibling of nitric oxide (NO) that targets distinct signalling pathways with pharmacological endpoints of high significance in the treatment of heart failure. Beneficial HNO effects depend, in part, on its ability to release calcitonin gene-related peptide (CGRP) through an unidentified mechanism. Here we propose that HNO is generated as a result of the reaction of the two gasotransmitters NO and H2S. We show that H2S and NO production colocalizes with transient receptor potential channel A1 (TRPA1), and that HNO activates the sensory chemoreceptor channel TRPA1 via formation of amino-terminal disulphide bonds, which results in sustained calcium influx. As a consequence, CGRP is released, which induces local and systemic vasodilation. H2S-evoked vasodilatatory effects largely depend on NO production and activation of HNO-TRPA1-CGRP pathway. We propose that this neuroendocrine HNO-TRPA1-CGRP signalling pathway constitutes an essential element for the control of vascular tone throughout the cardiovascular system.
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| 7. |
- Ebrahimi-Fakhari, Darius, et al.
(författare)
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Defining the clinical, molecular and imaging spectrum of adaptor protein complex 4-associated hereditary spastic paraplegia
- 2020
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Ingår i: Brain. - OXFORD ENGLAND : Oxford University Press (OUP). - 0006-8950 .- 1460-2156. ; 143:10, s. 2929-2944
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Tidskriftsartikel (refereegranskat)abstract
- Bi-allelic loss-of-function variants in genes that encode subunits of the adaptor protein complex 4 (AP-4) lead to prototypical yet poorly understood forms of childhood-onset and complex hereditary spastic paraplegia: SPG47 (AP4B1), SPG50 (AP4M1), SPG51 (AP4E1) and SPG52 (AP4S1). Here, we report a detailed cross-sectional analysis of clinical, imaging and molecular data of 156 patients from 101 families. Enrolled patients were of diverse ethnic backgrounds and covered a wide age range (1.0-49.3 years). While the mean age at symptom onset was 0.8 +/- 0.6 years [standard deviation (SD), range 0.2-5.0], the mean age at diagnosis was 10.2 +/- 8.5 years (SD, range 0.1-46.3). We define a set of core features: early-onset developmental delay with delayed motor milestones and significant speech delay (50% non-verbal); intellectual disability in the moderate to severe range; mild hypotonia in infancy followed by spastic diplegia (mean age: 8.4 +/- 5.1 years, SD) and later tetraplegia (mean age: 16.1 +/- 9.8 years, SD); postnatal microcephaly (83%); foot deformities (69%); and epilepsy (66%) that is intractable in a subset. At last follow-up, 36% ambulated with assistance (mean age: 8.9 +/- 6.4 years, SD) and 54% were wheelchair-dependent (mean age: 13.4 +/- 9.8 years, SD). Episodes of stereotypic laughing, possibly consistent with a pseudobulbar affect, were found in 56% of patients. Key features on neuroimaging include a thin corpus callosum (90%), ventriculomegaly (65%) often with colpocephaly, and periventricular white-matter signal abnormalities (68%). Iron deposition and polymicrogyria were found in a subset of patients. AP4B1-associated SPG47 and AP4M1-associated SPG50 accounted for the majority of cases. About two-thirds of patients were born to consanguineous parents, and 82% carried homozygous variants. Over 70 unique variants were present, the majority of which are frameshift or nonsense mutations. To track disease progression across the age spectrum, we defined the relationship between disease severity as measured by several rating scales and disease duration. We found that the presence of epilepsy, which manifested before the age of 3 years in the majority of patients, was associated with worse motor outcomes. Exploring genotype-phenotype correlations, we found that disease severity and major phenotypes were equally distributed among the four subtypes, establishing that SPG47, SPG50, SPG51 and SPG52 share a common phenotype, an 'AP-4 deficiency syndrome'. By delineating the core clinical, imaging, and molecular features of AP-4-associated hereditary spastic paraplegia across the age spectrum our results will facilitate early diagnosis, enable counselling and anticipatory guidance of affected families and help define endpoints for future interventional trials.
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| 8. |
- Herth, Felix J. F., et al.
(författare)
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Radiological and clinical outcomes of using Chartis (TM) to plan endobronchial valve treatment
- 2013
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Ingår i: European Respiratory Journal. - : European Respiratory Society (ERS). - 1399-3003 .- 0903-1936. ; 41:2, s. 302-308
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Tidskriftsartikel (refereegranskat)abstract
- One-way endobronchial valves (EBVs) have been shown to relieve symptoms of emphysema, particularly in patients without collateral ventilation (CV) between the target and adjacent lobes. In this study, we investigated the ability of the bronchoscopic Chartis (TM) Pulmonary Assessment System to predict treatment response by determining the presence of CV. 80 EBV patients underwent a pre-treatment Chartis assessment. Before and 30 days after implantation, high-resolution computed tomography scans were taken to determine target lobe volume reduction (TLVR). A pre- to post-treatment reduction of >= 350 mL was defined as significant. In addition, clinical outcomes (forced expiratory volume in 1 s (FEV1), 6-min walk test and St George's Respiratory Questionnaire) were compared over the same time period. Of the 51 patients classified as having an absence of CV according to their Chartis reading, 36 showed a TLVR 350 mL. 29 patients were classified as having CV, and of these 24 did not meet this TLVR cut-off. Chartis showed an accuracy level of 75% in predicting whether or not the TLVR cut-off would be reached. Those predicted to respond showed significantly greater TLVR (p<0.0001) and FEV1 improvement (p=0.0013) than those predicted not to respond. Chartis is a safe and effective method of predicting response to EBV treatment.
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| 9. |
- Hobson, Melissa J., et al.
(författare)
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TOI-199 b : A Well-characterized 100 day Transiting Warm Giant Planet with TTVs Seen from Antarctica
- 2023
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Ingår i: Astronomical Journal. - 0004-6256. ; 166:5
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Tidskriftsartikel (refereegranskat)abstract
- We present the spectroscopic confirmation and precise mass measurement of the warm giant planet TOI-199 b. This planet was first identified in TESS photometry and confirmed using ground-based photometry from ASTEP in Antarctica including a full 6.5 hr long transit, PEST, Hazelwood, and LCO; space photometry from NEOSSat; and radial velocities (RVs) from FEROS, HARPS, CORALIE, and CHIRON. Orbiting a late G-type star, TOI-199 b has a 104.854 − 0.002 + 0.001 day period, a mass of 0.17 ± 0.02 M J, and a radius of 0.810 ± 0.005 R J. It is the first warm exo-Saturn with a precisely determined mass and radius. The TESS and ASTEP transits show strong transit timing variations (TTVs), pointing to the existence of a second planet in the system. The joint analysis of the RVs and TTVs provides a unique solution for the nontransiting companion TOI-199 c, which has a period of 273.69 − 0.22 + 0.26 days and an estimated mass of 0.28 − 0.01 + 0.02 M J . This period places it within the conservative habitable zone.
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| 10. |
- Karis, O., et al.
(författare)
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High-kinetic-energy photoemission spectroscopy of Ni at 1s: 6-eV satellite at 4 eV
- 2008
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121 .- 1550-235X. ; 78:23, s. 3-3
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Tidskriftsartikel (refereegranskat)abstract
- Electron correlations are responsible for many profound phenomena in solid-state physics. A classical example is the 6-eV satellite in the photoelectron spectrum of Ni. Until now the satellite structure has only been investigated at the L shell and more shallow levels. Here we report a high-kinetic-energy photoemission spectroscopy (HIKE) investigation of Ni metal. We present 1s and 2p photoelectron spectra, obtained using excitation energies up to 12.6 keV. Our investigation demonstrates that the energy position of the satellite relative to the main line is different for the 1s and the 2p levels. In combination with electronic structure calculations, we show that this energy shift is attributed to unique differences in the core-valence coupling for the K and L-2,L-3 shells in 3d transition metals, resulting in different screening of the core holes.
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| 11. |
- Kemp, Samuel V., et al.
(författare)
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A Multicenter Randomized Controlled Trial of Zephyr Endobronchial Valve Treatment in Heterogeneous Emphysema (TRANSFORM)
- 2017
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Ingår i: American Journal of Respiratory and Critical Care Medicine. - : AMER THORACIC SOC. - 1073-449X .- 1535-4970. ; 196:12, s. 1535-1543
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Tidskriftsartikel (refereegranskat)abstract
- Rationale: Single-center randomized controlled trials of the Zephyr endobronchial valve (EBV) treatment have demonstrated benefit in severe heterogeneous emphysema. This is the first multicenter study evaluating this treatment approach. Objectives: To evaluate the efficacy and safety of Zephyr EBVs in patients with heterogeneous emphysema and absence of collateral ventilation.Methods: This was a prospective, multicenter 2:1 randomized controlled trial of EBVs plus standard of care or standard of care alone (SoC). Primary outcome at 3 months post-procedure was the percentage of subjects with FEV1 improvement from baseline of 12% or greater. Changes in FEV1, residual volume, 6-minute-walk distance, St. George's Respiratory Questionnaire score, and modified Medical Research Council score were assessed at 3 and 6 months, and target lobe volume reduction on chest computed tomography at 3 months.Measurements and Main Results: Ninety seven subjects were randomized toEBV(n = 65) or SoC(n = 32). At 3 months, 55.4% of EBV and 6.5% of SoC subjects had an FEV1 improvement of 12% or more (P < 0.001). Improvements were maintained at 6 months: EBV 56.3% versus SoC 3.2% (P < 0.001), with a mean +/- SD change in FEV1 at 6 months of 20.7 +/- 29.6% and -8.6 +/- 13.0%, respectively. A total of 89.8% of EBV subjects had target lobe volume reduction greater than or equal to 350 ml, mean 1.09 +/- 0.62 L (P < 0.001). Between-group differences for changes at 6 months were statistically and clinically significant: Delta EBV-SoC for residual volume, -700 ml; 6-minute-walk distance, +78.7 m; St. George's Respiratory Questionnaire score, -6.5 points; modified Medical Research Council dyspnea score, -0.6 points; and BODE(body mass index, airflow obstruction, dyspnea, and exercise capacity) index, 21.8 points (all P < 0.05). Pneumothorax was the most common adverse event, occurring in 19 of 65 (29.2%) of EBV subjects.Conclusions: EBV treatment in hyperinflated patients with heterogeneous emphysema without collateral ventilation resulted in clinically meaningful benefits in lung function, dyspnea, exercise tolerance, and quality of life, with an acceptable safety profile.
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| 12. |
- Söderström, Johan, et al.
(författare)
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Radiative decay spectra of selected doubly excited states in helium
- 2008
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Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics. - 1050-2947 .- 1094-1622. ; 77:1, s. 012513-
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Tidskriftsartikel (refereegranskat)abstract
- Radiative decay spectra of doubly excited states in He have been measured after selective excitation with monochromatized synchrotron radiation. The decay spectra are in excellent agreement with predictions based on calculations.
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| 13. |
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