| 1. |
- Esteve-Codina, Anna, et al.
(author)
-
Gender specific airway gene expression in COPD sub-phenotypes supports a role of mitochondria and of different types of leukocytes
- 2021
-
In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
-
Journal article (peer-reviewed)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.
|
|
| 2. |
|
|
| 3. |
- Grånäs, Elin, et al.
(author)
-
Water Chemistry beneath Graphene : Condensation of a Dense OH-H2O Phase under Graphene
- 2022
-
In: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 126:9, s. 4347-4354
-
Journal article (peer-reviewed)abstract
- Room temperature oxygen hydrogenation below graphene flakes supported by Ir(111) is investigated through a combination of X-ray photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory calculations using an evolutionary search algorithm. We demonstrate how the graphene cover and its doping level can be used to trap and characterize dense mixed O-OH-H2O phases that otherwise would not exist. Our study of these graphene-stabilized phases and their response to oxygen or hydrogen exposure reveals that additional oxygen can be dissolved into them at room temperature creating mixed O-OH-H2O phases with an increased areal coverage underneath graphene. In contrast, additional hydrogen exposure converts the mixed O-OH-H2O phases back to pure OH-H2O with a reduced areal coverage underneath graphene.
|
|
| 4. |
- Haitjema, Jarich, et al.
(author)
-
Soft X-ray absorption and fragmentation of tin-oxo cage photoresists
- 2024
-
In: Physical Chemistry Chemical Physics. - 1463-9076. ; 26:7, s. 5986-5998
-
Journal article (peer-reviewed)abstract
- “Tin-oxo cage” organometallic compounds are considered as photoresists for extreme ultraviolet (EUV) photolithography. To gain insight into their electronic structure and reactivity to ionizing radiation, we trapped bare gas-phase n-butyltin-oxo cage dications [(BuSn)12O14(OH)6]2+ in an ion trap and investigated their fragmentation upon soft X-ray photoabsorption by means of mass spectrometry. In complementary experiments, the tin-oxo cages with hydroxide and trifluoroacetate counter-anions were cast in thin films and studied using X-ray transmission spectroscopy. Quantum-chemical calculations were used to interpret the observed spectra. At the carbon K-edge, a distinct pre-edge absorption band can be attributed to transitions in which electrons are promoted from C1s orbitals to the lowest unoccupied molecular orbitals, which are delocalized orbitals with strong antibonding (Sn-C ?*) character. At higher energies, the most prominent resonant transitions involve C-C and C-H ?* valence states and Rydberg (3s and 3p) states. In the solid state, the onset of continuum ionization is shifted by ?5 eV to lower energy with respect to the gas phase, due to the electrostatic effect of the counterions. The O K-edge also shows a pre-edge absorption, but it is devoid of any specific features, because there are many transitions from the different O1s orbitals to a large number of vacant orbitals. In the gas phase, formation of the parent [(BuSn)12O14(OH)6]3+ radical ion is not observed at the C K-edge nor at the O K-edge, because the loss of a butyl group from this species is very efficient. We do observe a number of triply charged photofragment ions, some of which have lost up to 5 butyl groups. Structures of these species are proposed based on quantum-chemical calculations, and pathways of formation are discussed. Our results provide insight into the electronic structure of alkyltin-oxo cages, which is a prerequisite for understanding their response to EUV photons and their performance as EUV photoresists.
|
|
| 5. |
- Jones, Daniel O.B., et al.
(author)
-
Environment, ecology, and potential effectiveness of an area protected from deep-sea mining (Clarion Clipperton Zone, abyssal Pacific)
- 2021
-
In: Progress in Oceanography. - : Elsevier BV. - 0079-6611. ; 197:September-October 2021
-
Journal article (peer-reviewed)abstract
- To protect the range of habitats, species, and ecosystem functions in the Clarion Clipperton Zone (CCZ), a region of interest for deep-sea polymetallic nodule mining in the Pacific, nine Areas of Particular Environmental Interest (APEIs) have been designated by the International Seabed Authority (ISA). The APEIs are remote, rarely visited and poorly understood. Here we present and synthesise all available observations made at APEI-6, the most north eastern APEI in the network, and assess its representativity of mining contract areas in the eastern CCZ. The two studied regions of APEI-6 have a variable morphology, typical of the CCZ, with hills, plains and occasional seamounts. The seafloor is predominantly covered by fine-grained sediments, and includes small but abundant polymetallic nodules, as well as exposed bedrock. The oceanographic parameters investigated appear broadly similar across the region although some differences in deep-water mass separation were evident between APEI-6 and some contract areas. Sediment biogeochemistry is broadly similar across the area in the parameters investigated, except for oxygen penetration depth, which reached >2 m at the study sites within APEI-6, deeper than that found at UK1 and GSR contract areas. The ecology of study sites in APEI-6 differs from that reported from UK1 and TOML-D contract areas, with differences in community composition of microbes, macrofauna, xenophyophores and metazoan megafauna. Some species were shared between areas although connectivity appears limited. We show that, from the available information, APEI-6 is partially representative of the exploration areas to the south yet is distinctly different in several key characteristics. As a result, additional APEIs may be warranted and caution may need to be taken in relying on the APEI network alone for conservation, with other management activities required to help mitigate the impacts of mining in the CCZ.
|
|
| 6. |
|
|
| 7. |
- Myadam, Rahul, et al.
(author)
-
Risk of Adverse Outcomes Associated With Cardiac Sarcoidosis Diagnostic Schemes
- 2023
-
In: JACC: Clinical Electrophysiology. - 2405-500X. ; 9:8, s. 1719-1729
-
Journal article (peer-reviewed)abstract
- Background: Multiple cardiac sarcoidosis (CS) diagnostic schemes have been published. Objectives: This study aims to evaluate the association of different CS diagnostic schemes with adverse outcomes. The diagnostic schemes evaluated were 1993, 2006, and 2017 Japanese criteria and the 2014 Heart Rhythm Society criteria. Methods: Data were collected from the Cardiac Sarcoidosis Consortium, an international registry of CS patients. Outcome events were any of the following: all-cause mortality, left ventricular assist device placement, heart transplantation, and appropriate implantable cardioverter-defibrillator therapy. Logistic regression analysis evaluated the association of outcomes with each CS diagnostic scheme. Results: A total of 587 subjects met the following criteria: 1993 Japanese (n = 310, 52.8%), 2006 Japanese (n = 312, 53.2%), 2014 Heart Rhythm Society (n = 480, 81.8%), and 2017 Japanese (n = 112, 19.1%). Patients who met the 1993 criteria were more likely to experience an event than patients who did not (n = 109 of 310, 35.2% vs n = 59 of 277, 21.3%; OR: 2.00; 95% CI: 1.38-2.90; P < 0.001). Similarly, patients who met the 2006 criteria were more likely to have an event than patients who did not (n = 116 of 312, 37.2% vs n = 52 of 275, 18.9%; OR: 2.54; 95% CI: 1.74-3.71; P < 0.001). There was no statistically significant association between the occurrence of an event and whether a patient met the 2014 or the 2017 criteria (OR: 1.39; 95% CI: 0.85-2.27; P = 0.18 or OR: 1.51; 95% CI: 0.97-2.33; P = 0.067, respectively). Conclusions: CS patients who met the 1993 and the 2006 criteria had higher odds of adverse clinical outcomes. Future research is needed to prospectively evaluate existing diagnostic schemes and develop new risk models for this complex disease.
|
|
| 8. |
- Savary, Agata, et al.
(author)
-
PARSEME Corpus Release 1.3
- 2023
-
In: Proceedings of the 19th Workshop on Multiword Expressions (MWE 2023). - Stroudsburg : Association for Computational Linguistics. - 9781959429593 ; , s. 24-35
-
Conference paper (peer-reviewed)abstract
- We present version 1.3 of the PARSEME multilingual corpus annotated with verbal multiword expressions. Since the previous version, new languages have joined the undertaking of creating such a resource, some of the already existing corpora have been enriched with new annotated texts, while others have been enhanced in various ways. The PARSEME multilingual corpus represents 26 languages now. All monolingual corpora therein use Universal Dependencies v.2 tagset. They are (re-)split observing the PARSEME v.1.2 standard, which puts impact on unseen VMWEs. With the current iteration, the corpus release process has been detached from shared tasks; instead, a process for continuous improvement and systematic releases has been introduced.
|
|
| 9. |
- Schubert, Kaja, et al.
(author)
-
The electronic structure and deexcitation pathways of an isolated metalloporphyrin ion resolved by metal L-edge spectroscopy
- 2021
-
In: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 12:11, s. 3966-3976
-
Journal article (peer-reviewed)abstract
- The local electronic structure of the metal-active site and the deexcitation pathways of metalloporphyrins are crucial for numerous applications but difficult to access by commonly employed techniques. Here, we applied near-edge X-ray absorption mass spectrometry and quantum-mechanical restricted active space calculations to investigate the electronic structure of the metal-active site of the isolated cobalt(iii) protoporphyrin IX cation (CoPPIX+) and its deexcitation pathways upon resonant absorption at the cobalt L-edge. The experiments were carried out in the gas phase, thus allowing for control over the chemical state and molecular environment of the metalloporphyrin. The obtained mass spectra reveal that resonant excitations of CoPPIX+at the cobalt L3-edge lead predominantly to the formation of the intact radical dication and doubly charged fragments through losses of charged and neutral side chains from the macrocycle. The comparison between experiment and theory shows that CoPPIX+is in a3A2gtriplet ground state and that competing excitations to metal-centred non-bonding and antibonding σ* molecular orbitals lead to distinct deexcitation pathways.
|
|
