| 11. |
- Wang, Sen, et al.
(författare)
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ATAC-seq reveals the roles of chromatin accessibility in the chondrocytes of Kashin-Beck disease compared with primary osteoarthritis
- 2023
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Ingår i: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Objective: This study aimed to investigate the roles of accessible chromatin in understanding the different pathogeneses between Kashin-Beck disease (KBD) and primary osteoarthritis (OA).Methods: Articular cartilages of KBD and OA patients were collected, and after tissue digestion, primary chondrocytes were cultured in vitro. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) was performed to compare the accessible chromatin differences of chondrocytes between KBD and OA groups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were executed for the promoter genes. Then, the IntAct online database was used to generate networks of significant genes. Finally, we overlapped the analysis of differentially accessible region (DAR)-associated genes and differentially expressed genes (DEGs) obtained from whole-genomic microarray.Results: We obtained 2,751 total DARs, which contained 1,985 loss and 856 gain DARs and belonged to 11 location distributions. We obtained 218 motifs associated with loss DARs, 71 motifs associated with gain DARs, 30 motif enrichments of loss DARs, and 30 motif enrichments of gain DARs. In total, 1,749 genes are associated with loss DARs, and 826 genes are associated with gain DARs. Among them, 210 promoter genes are associated with loss DARs, and 112 promoter genes are associated with gain DARs. We obtained 15 terms of GO enrichment and 5 terms of KEGG pathway enrichment from loss DAR promoter genes, and 15 terms of GO enrichment and 3 terms of KEGG pathway enrichment from gain DAR promoter genes. We obtained CAPN6 and other 2 overlap genes from loss DARs-vs-down DEGs, AMOTL1 from gain DARs-vs-down DEGs, EBF3 and other 12 overlap genes from loss DARs-vs-up DEGs, and ADARB1 and other 10 overlap genes from 101 gain DARs-vs-up DEGs. These overlap genes were built into 4 gene interaction networks.Conclusion: FGF7, GPD1L, NFIB, RUNX2, and VCAM1 were the overlapped genes from the DAR-associated genes and DEGs. These genes were associated with the abnormal chondrocyte function, which may play crucial roles in different processes between KBD and OA in the way of accessible chromatin.
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| 12. |
- Wang, Yong, et al.
(författare)
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Characterization and formation mechanism of non-metallic inclusions in single bcc-phase high entropy alloy
- 2023
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Ingår i: Materials Characterization. - : Elsevier BV. - 1044-5803 .- 1873-4189. ; 205
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Tidskriftsartikel (refereegranskat)abstract
- This work aims to provide a fundamental study of inclusion characteristics in the single bcc-phase high entropy alloy (HEA), Mn-rich and Al-contained multicomponent system (Al-Cr-Mn-Fe-Co-Ni) was selected as the prototype alloy in this study. According to the differential thermal analysis (DTA) measurements, the solidus (TS) and liquidus (TL) temperatures of this alloy were in the range of 1225–1228 °C (1226 ± 2 °C) and 1268–1271 °C (1270 ± 2 °C), respectively. Non-metallic inclusions were investigated in a two-dimensional (2D) cross-section method as well as extracted by a three-dimensional (3D) electrolytic extraction method. It was found that AlN was the dominant inclusion phase, also a small amount of Al2O3 inclusions were observed. They formed in the liquid alloy and mostly presented as Al2O3-AlN agglomerates, where the size range of the AlN inclusions was larger than that of Al2O3. The theoretical calculation showed that AlN inclusion has a higher coagulation coefficient and collision rate than those of Al2O3 inclusions, which agrees well with the experimental observations. The inclusion characteristics of Al2O3 and AlN were closely related to the relative contents of O and N in the presence of high Al content in the alloy. The impurity elements of N and O were the key issues in controling the stable inclusion phase in high entropic alloy.
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| 13. |
- Xin, Tao, et al.
(författare)
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Time Series Recovery Using Adjacent Channel Data Based on LSTM: A Case Study of Subway Vibrations
- 2022
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Ingår i: Applied Sciences. - : MDPI. - 2076-3417. ; 12:22
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Tidskriftsartikel (refereegranskat)abstract
- Multi-sensor technology has been widely applied in the condition monitoring of rail transit. In practice, the data of some channels in the high channel counts are often abnormal or lost due to the abnormality and damage of the sensors, thus resulting in a large amount of data waste. A method for the data recovery of lost channels by using adjacent channel data is proposed to solve this problem. Based on the LSTM network algorithm, a data recovery model is established based on the “sequence-to-sequence” regression analysis of adjacent channel data. Taking the measured vibration data of a subway as an example, the network is trained with multi-channel measured data to recover the lost channel data of time-series characteristics. The results show that this multi-channel data recovery model is feasible, and the accuracy is up to 98%. This method can also further reduce the number of channels that need to be collected.
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| 14. |
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| 17. |
- Hayden, Michael R., et al.
(författare)
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The GALAH survey : chemical clocks
- 2022
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 517:4, s. 5325-5339
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Tidskriftsartikel (refereegranskat)abstract
- We present the first large-scale study that demonstrates how ages can be determined for large samples of stars through Galactic chemical evolution. Previous studies found that the elemental abundances of a star correlate directly with its age and metallicity. Using this knowledge, we derive ages for 214 577 stars in GALAH DR3 using only overall metallicities and chemical abundances. Stellar ages are estimated via the machine learning algorithm XGBoost for stars belonging to the Milky Way disc with metallicities in the range -1 < [Fe/H] < 0.5, using main-sequence turn-off stars as our training set. We find that stellar ages for the bulk of GALAH DR3 are precise to 1-2 Gyr using this method. With these ages, we replicate many recent results on the age-kinematic trends of the nearby disc, including the solar neighbourhood's age-velocity dispersion relationship and the larger global velocity dispersion relations of the disc found using Gaia and GALAH. These results show that chemical abundance variations at a given birth radius are small, and that strong chemical tagging of stars directly to birth clusters may prove difficult with our current elemental abundance precision. Our results highlight the need to measure abundances for as many nucleosynthetic production sites as possible in order to estimate reliable ages from chemistry. Our methods open a new door into studies of the kinematic structure and evolution of the disc, as ages may potentially be estimated to a precision of 1-2 Gyr for a large fraction of stars in existing spectroscopic surveys.
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| 18. |
- Hoencamp, Claire, et al.
(författare)
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3D genomics across the tree of life reveals condensin II as a determinant of architecture type
- 2021
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 372:6545, s. 984-989
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Tidskriftsartikel (refereegranskat)abstract
- We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
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| 19. |
- Joshi, Mrudula, et al.
(författare)
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Listening to patients, for the patients : The COVAD Study-Vision, organizational structure, and challenges
- 2024
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Ingår i: International Journal of Rheumatic Diseases. - : John Wiley & Sons. - 1756-1841 .- 1756-185X. ; 27:5
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Tidskriftsartikel (refereegranskat)abstract
- Background: The pandemic presented unique challenges for individuals with autoimmune and rheumatic diseases (AIRDs) due to their underlying condition, the effects of immunosuppressive treatments, and increased vaccine hesitancy.Objectives: The COVID-19 vaccination in autoimmune diseases (COVAD) study, a series of ongoing, patient self-reported surveys were conceived with the vision of being a unique tool to gather patient perspectives on AIRDs. It involved a multinational, multicenter collaborative effort amidst a global lockdown.Methods: Leveraging social media as a research tool, COVAD collected data using validated patient-reported outcomes (PROs). The study, comprising a core team, steering committee, and global collaborators, facilitated data collection and analysis. A pilot-tested, validated survey, featuring questions regarding COVID-19 infection, vaccination and outcomes, patient demographics, and PROs was circulated to patients with AIRDs and healthy controls (HCs).Discussion: We present the challenges encountered during this international collaborative project, including coordination, data management, funding constraints, language barriers, and authorship concerns, while highlighting the measures taken to address them.Conclusion: Collaborative virtual models offer a dynamic new frontier in medical research and are vital to studying rare diseases. The COVAD study demonstrates the potential of online platforms for conducting large-scale, patient-focused research and underscores the importance of integrating patient perspective into clinical care. Care of patients is our central motivation, and it is essential to recognize their voices as equal stakeholders and valued partners in the study of the conditions that affect them.
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| 20. |
- Kadam, Esha, et al.
(författare)
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Collating the voice of people with autoimmune diseases : Methodology for the Third Phase of the COVAD Studies
- 2024
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Ingår i: Rheumatology International. - : Springer. - 0172-8172 .- 1437-160X. ; 44:7, s. 1233-1244
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: The growing recognition of holistic patient care highlights the various factors shaping the quality of life of individuals with autoimmune and rheumatic diseases (AIRDs). Beyond the traditional disease measures, there is an emerging acknowledgment of the less-explored aspects, including subjective well-being, social determinants of health, comorbidities, mental health, and medication adherence. Moreover, digital health services have empowered patients to engage actively in decision-making alongside clinicians. To explore these domains within the context of AIRDs, the "Collating the Voice of People with Autoimmune Diseases" COVAD survey was conceived, a successor of the previous two COVAD surveys. In this document, we present the study protocol in comprehensive detail.METHODS: The COVAD-3 survey is a cross-sectional patient self-reported e-survey incorporating multiple widely accepted scales/scores to assess various aspects of patients' lifestyles objectively. To ensure the survey's accuracy and usability across diverse regions, it will be translated into multiple languages and subjected to rigorous vetting and pilot testing. It will be distributed by collaborators via online platforms and data will be collected from patients with AIRDs, and healthy individuals over eight months. Data analysis will focus on outcome measures related to various social, demographic, economic, and psychological factors.CONCLUSION: With the increasing awareness to adopt a holistic treatment approach encompassing all avenues of life, the COVAD-3 survey aims to gain valuable insights into the impact of social, demographic, economic, and psychological determinants of health on the subjective well-being in patients with AIRDs, which will contribute to a better understanding of their overall health and well-being.
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