| 1. |
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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Jin, Ying-Hui, et al.
(författare)
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Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
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Ingår i: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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| 5. |
- Aamodt, K., et al.
(författare)
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Alignment of the ALICE Inner Tracking System with cosmic-ray tracks
- 2010
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 5
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Konferensbidrag (refereegranskat)abstract
- ALICE (A Large Ion Collider Experiment) is the LHC (Large Hadron Collider) experiment devoted to investigating the strongly interacting matter created in nucleus-nucleus collisions at the LHC energies. The ALICE ITS, Inner Tracking System, consists of six cylindrical layers of silicon detectors with three different technologies; in the outward direction: two layers of pixel detectors, two layers each of drift, and strip detectors. The number of parameters to be determined in the spatial alignment of the 2198 sensor modules of the ITS is about 13,000. The target alignment precision is well below 10 mu m in some cases (pixels). The sources of alignment information include survey measurements, and the reconstructed tracks from cosmic rays and from proton-proton collisions. The main track-based alignment method uses the Millepede global approach. An iterative local method was developed and used as well. We present the results obtained for the ITS alignment using about 10(5) charged tracks from cosmic rays that have been collected during summer 2008, with the ALICE solenoidal magnet switched off.
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| 6. |
- Andersson, Anna, et al.
(författare)
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The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:4, s. 192-330
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Tidskriftsartikel (refereegranskat)abstract
- Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole-genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non-MLL-R cases) and 20 older children (MLL-R cases) with leukemia. Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases. Surprisingly, these mutations were often subclonal and were frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (mean of 6.5 mutations/case versus 1.3 mutations/case, P = 7.15 × 10(-5)) and had frequent mutations (45%) in epigenetic regulators, a category of genes that, with the exception of MLL, was rarely mutated in infant MLL-R ALL.
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| 7. |
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| 8. |
- Deng, Min, et al.
(författare)
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Genome-wide association analyses in Han Chinese identify two new susceptibility loci for amyotrophic lateral sclerosis
- 2013
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 45:6, s. 697-
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Tidskriftsartikel (refereegranskat)abstract
- To identify susceptibility genes for amyotrophic lateral sclerosis (ALS), we conducted a genome-wide association study (GWAS) in 506 individuals with sporadic ALS and 1,859 controls of Han Chinese ancestry. Ninety top SNPs suggested by the current GWAS and 6 SNPs identified by previous GWAS were analyzed in an independent cohort of 706 individuals with ALS and 1,777 controls of Han Chinese ancestry. We discovered two new susceptibility loci for ALS at 1q32 (CAMK1G, rs6703183, P-combined = 2.92 x 10(-8), odds ratio (OR) = 1.31) and 22p11 (CABIN1 and SUSD2, rs8141797, P-combined = 2.35 x 10(-9), OR = 1.52). These two loci explain 12.48% of the overall variance in disease risk in the Han Chinese population. We found no association evidence for the previously reported loci in the Han Chinese population, suggesting genetic heterogeneity of disease susceptibility for ALS between ancestry groups. Our study identifies two new susceptibility loci and suggests new pathogenic mechanisms of ALS.
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| 9. |
- DiBernardo, Allitia, et al.
(författare)
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Humanistic outcomes in treatment resistant depression : a secondary analysis of the STAR*D study
- 2018
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Ingår i: BMC Psychiatry. - : BMC. - 1471-244X. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundIn the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, a third of patients did not achieve remission or adequate response after two treatment trials, fulfilling requirements for treatment resistant depression (TRD). The present study is a secondary analysis of the STAR*D data conducted to compare the humanistic outcomes in patients with TRD and non-TRD MDD.MethodsPatients with major depressive disorder who entered level 3 of the STAR*D were included in the TRD group, while patients who responded to treatment and entered follow-up from level 1 or 2 were included in the non-TRD group. The first visit in level 1 was used for baseline assessments. The time-point of assessments for comparison was the first visit in level 3 for TRD patients (median day: 141), and the visit closest to 14160days from baseline for non-TRD patients. Outcomes were assessed by the 12-item Short Form Health Survey (SF12), 16-item Quality of Life Enjoyment and Satisfaction Questionnaire (Q-LES-Q), Work and Social Adjustment Scale (WSAS), and Work Productivity and Activity Impairment scale (WPAI). Scores were compared in a linear model with adjustment for covariates including age, gender, and depression severity measured by the 17-item Hamilton Rating Scale for Depression (HDRS17) and Quick Inventory of Depressive Symptomatology (QIDS).ResultsA total of 2467 (TRD: 377; non-TRD: 2090) patients were studied. TRD patients were slightly older (mean age 44 vs 42years), had a higher proportion of men (49% vs 37%, p<.0001), and baseline depression severity (HDRS17: 24.4 vs 22.0, p<.0001) vs non-TRD patients. During follow-up, TRD patients had lower health-related quality of life (HRQOL) scores on mental (30 vs 45.7) and physical components (47.7 vs 48.9) of the SF12, and lower Q-LES-Q scores (43.6 vs 63.7), greater functional and work impairments and productivity loss vs non-TRD patients (all p<0.05).Conclusion Patients with TRD had worse HRQOL, work productivity, and social functioning than the non-TRD patients.
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| 10. |
- Dong, Jiang, et al.
(författare)
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Arctic sea ice loss warmed the temperate East Asian winter in the mid-Holocene
- 2024
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Ingår i: Communications Earth and Environment. - 2662-4435. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- The recent colder winters in midlatitude Eurasia have been proposed to result from Arctic sea-ice decline. However, large uncertainties remain regarding this link in the present variable climate. Here, we present ice-rafted debris records from the eastern Arctic and geochemical data from the temperate East China Sea to reconstruct Holocene changes in sea ice and the East Asian winter monsoon. Our reconstructions and climate numerical simulations revealed enhanced Arctic sea-ice decline but warmer winters in East Asia in the mid-Holocene than in the late Holocene. In the warmer mid-Holocene, enhanced Arctic sea-ice loss transferred more heat from intensive summer solar insolation to the winter atmosphere, suppressing meridional heat transport; thus, less high-latitude cold air moved to lower latitudes in Asia due to the weakened winter monsoon. Our findings imply that the colder winters in East Asia may not change the long-term trend toward winter warming in the context of Arctic sea-ice decline.
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| 11. |
- Dries, Daniel R., et al.
(författare)
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Loss of Nicastrin from Oligodendrocytes Results in Hypomyelination and Schizophrenia with Compulsive Behavior
- 2016
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 291:22, s. 11647-11656
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Tidskriftsartikel (refereegranskat)abstract
- The biological underpinnings and the pathological lesions of psychiatric disorders are centuries-old questions that have yet to be understood. Recent studies suggest that schizophrenia and related disorders likely have their origins in perturbed neurodevelopment and can result from a large number of common genetic variants or multiple, individually rare genetic alterations. It is thus conceivable that key neurodevelopmental pathways underline the various genetic changes and the still unknown pathological lesions in schizophrenia. Here, we report that mice defective of the nicastrin subunit of gamma-secretase in oligodendrocytes have hypomyelination in the central nervous system. These mice have altered dopamine signaling and display profound abnormal phenotypes reminiscent of schizophrenia. In addition, we identify an association of the nicastrin gene with a human schizophrenia cohort. These observations implicate gamma-secretase and its mediated neurodevelopmental pathways in schizophrenia and provide support for the "myelination hypothesis" of the disease. Moreover, by showing that schizophrenia and obsessive-compulsive symptoms could be modeled in animals wherein a single genetic factor is altered, our work provides a biological basis that schizophrenia with obsessive-compulsive disorder is a distinct subtype of schizophrenia.
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| 12. |
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| 13. |
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| 14. |
- Harris, Valerie M., et al.
(författare)
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Klinefelters syndrome (47,XXY) is in excess among men with Sjogrens syndrome
- 2016
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Ingår i: Clinical Immunology. - : ACADEMIC PRESS INC ELSEVIER SCIENCE. - 1521-6616 .- 1521-7035. ; 168, s. 25-29
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Tidskriftsartikel (refereegranskat)abstract
- Primary Sjogrens syndrome (pSS) has a strong female bias. We evaluated an X chromosome dose effect by analyzing 47,XXY (Klinefelters syndrome, 1 in 500 live male births) among subjects with pSS. 47,XXY was determined by examination of fluorescence intensity of single nucleotide polymorphisms from the X and Y chromosomes. Among 136 pSS men there were 4 with 47,XXY. This was significantly different from healthy controls (1 of 1254 had 47)0(Y, p = 0.0012 by Fishers exact test) as well men with rheumatoid arthritis (0 of 363 with 47,XXY), but not different compared to men with systemic lupus erythematosus (SLE) (4 of 136 versus 8 of 306, Fishers exact test p = NS). These results are consistent with the hypothesis that the number of X chromosomes is critical for the female bias of pSS, a property that may be shared with SLE but not RA. Published by Elsevier Inc.
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| 15. |
- Holmfeldt, Linda, et al.
(författare)
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The genomic landscape of hypodiploid acute lymphoblastic leukemia
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:3, s. 242-252
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Tidskriftsartikel (refereegranskat)abstract
- The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole-genome and exome sequencing of 40 cases, identified two subtypes that differ in the severity of aneuploidy, transcriptional profiles and submicroscopic genetic alterations. Near-haploid ALL with 24-31 chromosomes harbor alterations targeting receptor tyrosine kinase signaling and Ras signaling (71%) and the lymphoid transcription factor gene IKZF3 (encoding AIOLOS; 13%). In contrast, low-hypodiploid ALL with 32-39 chromosomes are characterized by alterations in TP53 (91.2%) that are commonly present in nontumor cells, IKZF2 (encoding HELIOS; 53%) and RB1 (41%). Both near-haploid and low-hypodiploid leukemic cells show activation of Ras-signaling and phosphoinositide 3-kinase (PI3K)-signaling pathways and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia.
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| 16. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 17. |
- Kottyan, Leah C., et al.
(författare)
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The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share.
- 2015
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 24:2, s. 582-596
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Tidskriftsartikel (refereegranskat)abstract
- Exploiting genotyping, DNA sequencing, imputation and trans-ancestral mapping, we used Bayesian and frequentist approaches to model the IRF5-TNPO3 locus association, now implicated in two immunotherapies and seven autoimmune diseases. Specifically, in systemic lupus erythematosus (SLE), we resolved separate associations in the IRF5 promoter (all ancestries) and with an extended European haplotype. We captured 3230 IRF5-TNPO3 high-quality, common variants across 5 ethnicities in 8395 SLE cases and 7367 controls. The genetic effect from the IRF5 promoter can be explained by any one of four variants in 5.7 kb (P-valuemeta = 6 × 10(-49); OR = 1.38-1.97). The second genetic effect spanned an 85.5-kb, 24-variant haplotype that included the genes IRF5 and TNPO3 (P-valuesEU = 10(-27)-10(-32), OR = 1.7-1.81). Many variants at the IRF5 locus with previously assigned biological function are not members of either final credible set of potential causal variants identified herein. In addition to the known biologically functional variants, we demonstrated that the risk allele of rs4728142, a variant in the promoter among the lowest frequentist probability and highest Bayesian posterior probability, was correlated with IRF5 expression and differentially binds the transcription factor ZBTB3. Our analytical strategy provides a novel framework for future studies aimed at dissecting etiological genetic effects. Finally, both SLE elements of the statistical model appear to operate in Sjögrens syndrome and systemic sclerosis whereas only the IRF5-TNPO3 gene-spanning haplotype is associated with primary biliary cirrhosis, demonstrating the nuance of similarity and difference in autoimmune disease risk mechanisms at IRF5-TNPO3.
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| 18. |
- Li, Feiran, 1993, et al.
(författare)
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Deep learning-based k(cat) prediction enables improved enzyme-constrained model reconstruction
- 2022
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Ingår i: Nature Catalysis. - : Springer Science and Business Media LLC. - 2520-1158. ; 5:8, s. 662-672
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Tidskriftsartikel (refereegranskat)abstract
- Enzyme turnover numbers (k(cat)) are key to understanding cellular metabolism, proteome allocation and physiological diversity, but experimentally measured k(cat) data are sparse and noisy. Here we provide a deep learning approach (DLKcat) for high-throughput k(cat) prediction for metabolic enzymes from any organism merely from substrate structures and protein sequences. DLKcat can capture k(cat) changes for mutated enzymes and identify amino acid residues with a strong impact on k(cat) values. We applied this approach to predict genome-scale k(cat) values for more than 300 yeast species. Additionally, we designed a Bayesian pipeline to parameterize enzyme-constrained genome-scale metabolic models from predicted k(cat) values. The resulting models outperformed the corresponding original enzyme-constrained genome-scale metabolic models from previous pipelines in predicting phenotypes and proteomes, and enabled us to explain phenotypic differences. DLKcat and the enzyme-constrained genome-scale metabolic model construction pipeline are valuable tools to uncover global trends of enzyme kinetics and physiological diversity, and to further elucidate cellular metabolism on a large scale.
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| 19. |
- Li, Qian, et al.
(författare)
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Genome-wide identification of resistance genes and cellular analysis of key gene knockout strain under 5-hydroxymethylfurfural stress in Saccharomyces cerevisiae
- 2023
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Ingår i: BMC Microbiology. - 1471-2180. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- In bioethanol production, the main by-product, 5-hydroxymethylfurfural (HMF), significantly hinders microbial fermentation. Therefore, it is crucial to explore genes related to HMF tolerance in Saccharomyces cerevisiae for enhancing the tolerance of ethanol fermentation strains. A comprehensive analysis was conducted using genome-wide deletion library scanning and SGAtools, resulting in the identification of 294 genes associated with HMF tolerance in S. cerevisiae. Further KEGG and GO enrichment analysis revealed the involvement of genes OCA1 and SIW14 in the protein phosphorylation pathway, underscoring their role in HMF tolerance. Spot test validation and subcellular structure observation demonstrated that, following a 3-h treatment with 60mM HMF, the SIW14 gene knockout strain exhibited a 12.68% increase in cells with abnormal endoplasmic reticulum (ER) and a 22.41% increase in the accumulation of reactive oxygen species compared to the BY4741 strain. These findings indicate that the SIW14 gene contributes to the protection of the ER structure within the cell and facilitates the clearance of reactive oxygen species, thereby confirming its significance as a key gene for HMF tolerance in S. cerevisiae.
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| 20. |
- Lindblad, Oscar, et al.
(författare)
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BEX1 acts as a tumor suppressor in acute myeloid leukemia.
- 2015
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Ingår i: Oncotarget. - 1949-2553. ; 6:25, s. 21395-21405
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Tidskriftsartikel (refereegranskat)abstract
- Acute myeloid leukemia (AML) is a heterogeneous disease of the myeloid lineage. About 35% of AML patients carry an oncogenic FLT3 mutant making FLT3 an attractive target for treatment of AML. Major problems in the development of FLT3 inhibitors include lack of specificity, poor response and development of a resistant phenotype upon treatment. Further understanding of FLT3 signaling and discovery of novel regulators will therefore help to determine additional pharmacological targets in FLT3-driven AML. In this report, we identified BEX1 as a novel regulator of oncogenic FLT3-ITD-driven AML. We showed that BEX1 expression was down-regulated in a group of AML patients carrying FLT3-ITD. Loss of BEX1 expression resulted in poor overall survival (hazard ratio, HR = 2.242, p = 0.0011). Overexpression of BEX1 in mouse pro-B and myeloid cells resulted in decreased FLT3-ITD-dependent cell proliferation, colony and tumor formation, and in increased apoptosis in vitro and in vivo. BEX1 localized to the cytosolic compartment of cells and significantly decreased FLT3-ITD-induced AKT phosphorylation without affecting ERK1/2 or STAT5 phosphorylation. Our data suggest that the loss of BEX1 expression in FLT3-ITD driven AML potentiates oncogenic signaling and leads to decreased overall survival of the patients.
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| 21. |
- Liu, Ke, et al.
(författare)
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X Chromosome Dose and Sex Bias in Autoimmune Diseases
- 2016
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Ingår i: Arthritis & Rheumatology. - : WILEY-BLACKWELL. - 2326-5191 .- 2326-5205. ; 68:5, s. 1290-1300
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Tidskriftsartikel (refereegranskat)abstract
- Objective. More than 80% of autoimmune disease predominantly affects females, but the mechanism for this female bias is poorly understood. We suspected that an X chromosome dose effect accounts for this, and we undertook this study to test our hypothesis that trisomy X (47, XXX; occurring in similar to 1 in 1,000 live female births) would be increased in patients with female-predominant diseases (systemic lupus erythematosus [SLE], primary Sjogrens syndrome [SS], primary biliary cirrhosis, and rheumatoid arthritis [RA]) compared to patients with diseases without female predominance (sarcoidosis) and compared to controls. Methods. All subjects in this study were female. We identified subjects with 47, XXX using aggregate data from single-nucleotide polymorphism arrays, and, when possible, we confirmed the presence of 47, XXX using fluorescence in situ hybridization or quantitative polymerase chain reaction. Results. We found 47, XXX in 7 of 2,826 SLE patients and in 3 of 1,033 SS patients, but in only 2 of 7,074 controls (odds ratio in the SLE and primary SS groups 8.78 [95% confidence interval 1.67-86.79], P = 0.003 and odds ratio 10.29 [95% confidence interval 1.18-123.47], P = 0.02, respectively). One in 404 women with SLE and 1 in 344 women with SS had 47, XXX. There was an excess of 47, XXX among SLE and SS patients. Conclusion. The estimated prevalence of SLE and SS in women with 47, XXX was similar to 2.5 and similar to 2.9 times higher, respectively, than that in women with 46, XX and similar to 25 and similar to 41 times higher, respectively, than that in men with 46, XY. No statistically significant increase of 47, XXX was observed in other female-biased diseases (primary biliary cirrhosis or RA), supporting the idea of multiple pathways to sex bias in autoimmunity.
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| 22. |
- Liu, Ke, et al.
(författare)
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X Chromosome Dose and Sex Bias in Autoimmune Diseases : Increased 47,XXX in Systemic Lupus Erythematosus and Sjögren's Syndrome
- 2016
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Ingår i: Arthritis & Rheumatology. - : Wiley. - 2326-5191 .- 2326-5205. ; 68:5, s. 1290-1300
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE:More than 80% of autoimmune disease is female dominant, but the mechanism for this female bias is poorly understood. We suspected an X chromosome dose effect and hypothesized that trisomy X (47,XXX, 1 in ∼1,000 live female births) would be increased in female predominant diseases (e.g. systemic lupus erythematosus [SLE], primary Sjögren's syndrome [SS], primary biliary cirrhosis [PBC] and rheumatoid arthritis [RA]) compared to diseases without female predominance (sarcoidosis) and controls.METHODS:We identified 47,XXX subjects using aggregate data from single nucleotide polymorphism (SNP) arrays and confirmed, when possible, by fluorescent in situ hybridization (FISH) or quantitative polymerase chain reaction (q-PCR).RESULTS:We found 47,XXX in seven of 2,826 SLE and three of 1,033 SS female patients, but only in two of the 7,074 female controls (p=0.003, OR=8.78, 95% CI: 1.67-86.79 and p=0.02, OR=10.29, 95% CI: 1.18-123.47; respectively). One 47,XXX subject was present for ∼404 SLE women and ∼344 SS women. 47,XXX was present in excess among SLE and SS subjects.CONCLUSION:The estimated prevalence of SLE and SS in women with 47,XXX was respectively ∼2.5 and ∼2.9 times higher than in 46,XX women and ∼25 and ∼41 times higher than in 46,XY men. No statistically significant increase of 47,XXX was observed in other female-biased diseases (PBC or RA), supporting the idea of multiple pathways to sex bias in autoimmunity. This article is protected by copyright. All rights reserved.
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| 23. |
- Liu, Tao, et al.
(författare)
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16% efficiency all-polymer organic solar cells enabled by a finely tuned morphology via the design of ternary blend
- 2021
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Ingår i: Joule. - : CELL PRESS. - 2542-4351. ; 5:4, s. 914-930
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Tidskriftsartikel (refereegranskat)abstract
- A SUMMARY There is an urgent demand for all-polymer organic solar cells (AP-OSCs) to gain higher efficiency. Here, we successfully improve the performance to 16.09% by introducing a small amount of BN-T, a B <- N-type polymer acceptor, into the PM6:PY-IT blend. It has been found that BN-T makes the active layer, based on the PM6:PY-IT:BN-T ternary blend, more crystalline but meanwhile slightly reduces the phase separation, leading to enhancement of both exciton harvesting and charge transport. From a thermodynamic viewpoint, BN-T prefers to reside between PM6 and PY-IT, and the fraction of this fine-tunes the morphology. Besides, a significantly reduced nonradiative energy loss occurs in the ternary blend, along with the coexistence of energy and charge transfer between the two acceptors. The progressive performance facilitated by these improved properties demonstrates that AP-OSCs can possibly comparably efficient with those based on small molecule acceptors, further enhancing the competitiveness of this device type.
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| 24. |
- Liu, Yang, et al.
(författare)
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MiR-378a suppresses tenogenic differentiation and tendon repair by targeting at TGF-β2
- 2019
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Ingår i: Stem Cell Research and Therapy. - : Springer Science and Business Media LLC. - 1757-6512. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Tendons are a crucial component of the musculoskeletal system and responsible for transmission forces derived from muscle to bone. Patients with tendon injuries are often observed with decreased collagen production and matrix degeneration, and healing of tendon injuries remains a challenge as a result of limited understanding of tendon biology. Recent studies highlight the contribution of miR-378a on the regulation gene expression during tendon differentiation. Methods: We examined the tendon microstructure and tendon repair with using miR-378a knock-in transgenic mice, and the tendon-derived stem cells were also isolated from transgenic mice to study their tenogenic differentiation ability. Meanwhile, the expression levels of tenogenic markers were also examined in mouse tendon-derived stem cells transfected with miR-378a mimics during tenogenic differentiation. With using online prediction software and luciferase reporter assay, the binding target of miR-378a was also studied. Results: Our results indicated miR-378a impairs tenogenic differentiation and tendon repair by inhibition collagen and extracellular matrix production both in vitro and in vivo. We also demonstrated that miR-378a exert its inhibitory role during tenogenic differentiation through binding at TGFβ2 by luciferase reporter assay and western blot. Conclusions: Our investigation suggests that miR-378a could be considered as a new potential biomarker for tendon injury diagnosis or drug target for a possible therapeutic approach in future clinical practice.
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| 25. |
- Lu, Hongzhong, 1987, et al.
(författare)
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A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 and an associated ecosystem of models that represent a comprehensive computational resource for performing simulations of the metabolism of Saccharomyces cerevisiae––an important model organism and widely used cell-factory. Yeast8 tracks community development with version control, setting a standard for how GEMs can be continuously updated in a simple and reproducible way. We use Yeast8 to develop the derived models panYeast8 and coreYeast8, which in turn enable the reconstruction of GEMs for 1,011 different yeast strains. Through integration with enzyme constraints (ecYeast8) and protein 3D structures (proYeast8DB), Yeast8 further facilitates the exploration of yeast metabolism at a multi-scale level, enabling prediction of how single nucleotide variations translate to phenotypic traits.
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| 26. |
- Lu, Hongzhong, 1987, et al.
(författare)
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Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection
- 2021
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Ingår i: Molecular Systems Biology. - : EMBO. - 1744-4292. ; 17:10
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Tidskriftsartikel (refereegranskat)abstract
- Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome-scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence-level evolution has shaped reaction networks towards new metabolic functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer and gene duplication, onto relevant subpathways to explain metabolic plasticity. This demonstrates that gene family expansion and enzyme promiscuity are prominent mechanisms for metabolic trait gains, while GEM simulations reveal that additional factors, such as gene loss from distant pathways, contribute to trait losses. Furthermore, our analysis could pinpoint to specific genes and pathways that have been under positive selection and relevant for the formulation of complex metabolic traits, i.e. thermotolerance and the Crabtree effect. Our findings illustrate how multidimensional evolution in both metabolic network structure and individual enzymes drives phenotypic variations.
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| 27. |
- Lu, Jing, et al.
(författare)
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Ameliorated Snake Optimizer-Based Approximate Merging of Disk Wang-Ball Curves
- 2024
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Ingår i: Biomimetics. - : MDPI. - 2313-7673. ; 9:3
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Tidskriftsartikel (refereegranskat)abstract
- A method for the approximate merging of disk Wang-Ball (DWB) curves based on the modified snake optimizer (BEESO) is proposed in this paper to address the problem of difficulties in the merging of DWB curves. By extending the approximate merging problem for traditional curves to disk curves and viewing it as an optimization problem, an approximate merging model is established to minimize the merging error through an error formulation. Considering the complexity of the model built, a BEESO with better convergence accuracy and convergence speed is introduced, which combines the snake optimizer (SO) and three strategies including bi-directional search, evolutionary population dynamics, and elite opposition-based learning. The merging results and merging errors of numerical examples demonstrate that BEESO is effective in solving approximate merging models, and it provides a new method for the compression and transfer of product shape data in Computer-Aided Geometric Design.
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| 28. |
- Lu, Xiao-Gang, et al.
(författare)
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Calculations of thermophysical properties of cubic carbides and nitrides using Debye-Grüneisen model
- 2007
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Ingår i: Acta Materialia. - : Elsevier BV. - 1359-6454 .- 1873-2453. ; 55:4, s. 1215-1226
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Tidskriftsartikel (refereegranskat)abstract
- The thermal expansivities and heat capacities of NIX (M = Ti, Zr, Hf, V, Nb, Ta; X = C, N) carbides and nitrides with NaCl structure were calculated using the Debye-Gruneisen model combined with ab initio calculations. Two different approximations for the Gruneisen parameter gamma were used in the Debye-Gruneisen model, i.e. the expressions proposed by Slater and by Dugdale and MacDonald. The thermal electronic contribution was evaluated from ab initio calculations of the electronic density of states. The calculated results were compared with CALPHAD assessments and experimental data. It was found that the calculations using the Dugdale-MacDonald gamma can account for most of the experimental data. By fitting experimental heat capacity and thermal expansivity data below the Debye temperatures, an estimation of Poisson's ratio was obtained and Young's and shear moduli were evaluated. In order to reach a reasonable agreement with experimental data, it was necessary to use the logarithmic averaged mass of the constituent atoms. The agreements between the calculated and the experimental values for the bulk and Young's moduli are generally better than the agreement for shear modulus.
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| 29. |
- Lu, Xiao-Gang, 1970-
(författare)
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Theoretical modeling of molar volume and thermal expansion
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Combination of the Calphad method and theoretical calculations provides new possibilities for the study of materials science. This work is a part of the efforts within the CCT project (Centre of Computational Thermodynamics) to combine these methods to facilitate modeling and to extend the thermodynamic databases with critically assessed volume data. In this work, the theoretical calculations refer to first-principles and Debye-Grüneisen calculations. The first-principles (i.e. ab initio) electronic structure calculations, based on the Density- Functional Theory (DFT), are capable of predicting various physical properties at 0 K, such as formation energy, volume and bulk modulus. The ab initio simulation software, VASP, was used to calculate the binding curves (i.e. equation of state at 0 K) of metallic elements, cubic carbides and nitrides. From the binding curves, the equilibrium volumes at 0 K were calculated for several metastable structures as well as stable structures. The vibrational contribution to the free energy was calculated using the Debye-Grüneisen model combined with first-principles calculations. Two different approximations for the Grüneisen parameter, γ, were used in the Debye-Grüneisen model, i.e. Slater’s and Dugdale-MacDonald’s expressions. The thermal electronic contribution was evaluated from the calculated electronic density of states. The calculated thermal expansivities for metallic elements, cubic carbides and nitrides were compared with Calphad assessments. It was found that the experimental data are within the limits of the calculations using the two approximations for γ. By fitting experimental heat capacity and thermal expansivity around Debye temperatures, we obtained optimal Poisson’s ratio values and used them to evaluate Young’s and Shear moduli. In order to reach a reasonable agreement with the experiments, it is necessary to use the logarithmic averaged mass of the constitutional atoms. The agreements between the calculations and experiments are generally better for bulk modulus and Young’s modulus than that for shear modulus. A new model describing thermodynamic properties at high pressures was implemented in Thermo-Calc. The model is based on an empirical relation between volume and isothermal bulk modulus. Pure Fe and solid MgO were assessed using this model. Solution phases will be considered in a future work to check the model for compositional dependence.
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| 30. |
- Lu, Xiao-Gang, et al.
(författare)
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Theoretical modeling of molar volume and thermal expansion
- 2005
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Ingår i: Acta Materialia. - : Elsevier BV. - 1359-6454 .- 1873-2453. ; 53:8, s. 2259-2272
-
Tidskriftsartikel (refereegranskat)abstract
- The molar volumes and thermal expansions of transition cubic metals were studied by means of the Calphad approach and the Debye-Gruneisen model. Experimental data were collected and assessed using Calphad procedures, and consistent results were obtained which give the best description of all experimental data. In order to put the prediction of the thermodynamic properties of metastable phases on a sound physical basis, the Debye-Gruneisen model was chosen to account for the vibrational contribution and calculate the coefficients of linear thermal expansion (CLEs) of stable cubic metals. Two approximations for Gruneisen parameter gamma, i.e. Slater ' s and Dugdale and MacDonald ' s expressions were adopted. A modified calculation scheme, first proposed by Wang et al., was derived in a straightforward way and used to evaluate the Debye temperature from ab initio electronic total-energy calculations at T = 0 K. The thermal electronic contribution to CLE was also evaluated from the electronic density of states. The calculated total CLEs were compared with those from the Calphad assessments. A satisfactory agreement is reached.
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| 31. |
- Lu, Xiao-Gang, et al.
(författare)
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Thermodynamic assessments of the Ni-Pt and Al-Ni-Pt systems
- 2009
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Ingår i: Calphad. - : Elsevier BV. - 0364-5916 .- 1873-2984. ; 33:3, s. 450-456
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Tidskriftsartikel (refereegranskat)abstract
- The Ni-Pt system is assessed using the CALPHAD method. The four fcc-based phases, i.e. disordered solid solution phase, Ni3Pt-L1(2), NiPt-L1(0) and NiPt3-L1(2), are described by a four-sublattice model. The calculated thermodynamic properties and order/disorder phase transformations are in good agreement with the experimental data. In order to facilitate the assessment, first-principles pseudopotential calculations are also performed to calculate the enthalpy of formation at 0 K, and comparison with the assessed values is discussed. By combining the assessments of Al-Ni and Al-Pt, the Al-Ni-Pt ternary system is assessed within a narrow temperature range, focusing on the fcc-based phases and their phase equilibria with B2 phase.
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| 32. |
- Ma, Ruijie, et al.
(författare)
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All-polymer solar cells with over 16% efficiency and enhanced stability enabled by compatible solvent and polymer additives
- 2022
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Ingår i: Aggregate. - : Wiley. - 2692-4560 .- 2766-8541. ; 3:3
-
Tidskriftsartikel (refereegranskat)abstract
- Considering the robust and stable nature of the active layers, advancing the power conversion efficiency (PCE) has long been the priority for all-polymer solar cells (all-PSCs). Despite the recent surge of PCE, the photovoltaic parameters of the state-of-the-art all-PSC still lag those of the polymer:small molecule-based devices. To compete with the counterparts, judicious modulation of the morphology and thus the device electrical properties are needed. It is difficult to improve all the parameters concurrently for the all-PSCs with advanced efficiency, and one increase is typically accompanied by the drop of the other(s). In this work, with the aids of the solvent additive (1-chloronaphthalene) and the n-type polymer additive (N2200), we can fine-tune the morphology of the active layer and demonstrate a 16.04% efficient all-PSC based on the PM6:PY-IT active layer. The grazing incidence wide-angle X-ray scattering measurements show that the shape of the crystallites can be altered, and the reshaped crystallites lead to enhanced and more balanced charge transport, reduced recombination, and suppressed energy loss, which lead to concurrently improved and device efficiency and stability.
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| 33. |
- Mlynczak, Martin G., et al.
(författare)
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Energy transport in the thermosphere during the solar storms of April 2002
- 2005
-
Ingår i: Journal of Geophysical Research - Space Physics. - 2169-9380 .- 2169-9402. ; 110:A12
-
Tidskriftsartikel (refereegranskat)abstract
- The dramatic solar storm events of April 2002 deposited a large amount of energy into the Earth's upper atmosphere, substantially altering the thermal structure, the chemical composition, the dynamics, and the radiative environment. We examine the flow of energy within the thermosphere during this storm period from the perspective of infrared radiation transport and heat conduction. Observations from the SABER instrument on the TIMED satellite are coupled with computations based on the ASPEN thermospheric general circulation model to assess the energy flow. The dominant radiative response is associated with dramatically enhanced infrared emission from nitric oxide at 5.3 μm from which a total of ∼7.7 × 1023 ergs of energy are radiated during the storm. Energy loss rates due to NO emission exceed 2200 Kelvin per day. In contrast, energy loss from carbon dioxide emission at 15 μm is only ∼2.3% that of nitric oxide. Atomic oxygen emission at 63 μm is essentially constant during the storm. Energy loss from molecular heat conduction may be as large as 3.8% of the NO emission. These results confirm the “natural thermostat” effect of nitric oxide emission as the primary mechanism by which storm energy is lost from the thermosphere below 210 km.
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| 34. |
- Pan, Liang, et al.
(författare)
-
a A Resistance-Switchable and Ferroelectric Metal Organic Framework
- 2014
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 136:50, s. 17477-17483
-
Tidskriftsartikel (refereegranskat)abstract
- The ever-emerging demands on miniaturization of electronic devices have pushed the development of innovative materials with desired properties. One major endeavor is the development of organic- or organic-inorganic hybrid-based electronics as alternatives or supplements to silicon-based devices. Herein we report the first observation of the coexistence of resistance switching and ferroelectricity in a metal-organic framework (MOF) material, [InC16H11N2O8]center dot 1.5H(2)O, denoted as RSMOF-1. The electrical resistance of RSMOF-1 can be turned on and off repeatedly with a current ratio of 30. A first-principles molecular dynamics simulation suggests that the resistive switching effect is related to the ferroelectric transition of N center dot center dot center dot H-O center dot center dot center dot H-N bridge-structured dipoles of the guest water molecules and the amino-tethered MOF nanochannel. The discovery of the resistive switching effect and ferroelectricity in MOFs offers great potential for the physical implementation of novel electronics for next-generation digital processing and communication.
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| 35. |
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| 36. |
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| 37. |
- Rosenqvist, Lisa, et al.
(författare)
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Magnetospheric energy budget during huge geomagnetic activity using Cluster and ground-based data
- 2006
-
Ingår i: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 111:A10
-
Tidskriftsartikel (refereegranskat)abstract
- The Cluster spacecraft crossed the magnetopause at the duskward flank of the tail while the European Incoherent Scatter (EISCAT) radars and magnetometers observed the ionosphere during a sequence of intense substorm-like geomagnetic activity in October 2003. We attempt to estimate the local and global energy flow from the magnetosheath into the magnetotail and the ionosphere under these extreme conditions. We make for the first time direct observational estimates of the local solar wind power input using Cluster measurements. The global power input based on Cluster observations was found to be between 17 and 40 TW at the onset of the substorm intensification. However, spacecraft observations and global modelling of the magnetotail suggest that it is most probably closer to 17 TW. This is more than two times lower than the predicted epsilon parameter value ( 37 TW). Energy deposition in the ionosphere has been estimated locally with EISCAT and globally with the assimilated mapping of ionospheric electrodynamics (AMIE) technique. The amount of the global solar wind power input ( 17 TW) that is dissipated via Joule heating in the ionosphere is found to be 30%. The corresponding ratio based on empirical estimates is only 3%. However, empirical proxies seem to underestimate the magnitude of the Joule heating rate as compared to AMIE estimates (similar to a factor 4) and the epsilon parameter is more than twice as large as the Cluster estimate. In summary, the observational estimates provide a good balance between the energy input to the magnetosphere and deposition in the ionosphere. Empirical proxies seem to suffer from overestimations ( epsilon parameter) and underestimations ( Joule heating proxies) when pushed to the extreme circumstances during the early main phase of this storm period.
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| 38. |
- Sarris, Theodore E., et al.
(författare)
-
Daedalus MASE (mission assessment through simulation exercise): A toolset for analysis of in situ missions and for processing global circulation model outputs in the lower thermosphere-ionosphere
- 2023
-
Ingår i: Frontiers in Astronomy and Space Sciences. - : Frontiers Media SA. - 2296-987X. ; 9
-
Tidskriftsartikel (refereegranskat)abstract
- Daedalus MASE (Mission Assessment through Simulation Exercise) is an open-source package of scientific analysis tools aimed at research in the Lower Thermosphere-Ionosphere (LTI). It was created with the purpose to assess the performance and demonstrate closure of the mission objectives of Daedalus, a mission concept targeting to perform in-situ measurements in the LTI. However, through its successful usage as a mission-simulator toolset, Daedalus MASE has evolved to encompass numerous capabilities related to LTI science and modeling. Inputs are geophysical observables in the LTI, which can be obtained either through in-situ measurements from spacecraft and rockets, or through Global Circulation Models (GCM). These include ion, neutral and electron densities, ion and neutral composition, ion, electron and neutral temperatures, ion drifts, neutral winds, electric field, and magnetic field. In the examples presented, these geophysical observables are obtained through NCAR’s Thermosphere-Ionosphere-Electrodynamics General Circulation Model. Capabilities of Daedalus MASE include: 1) Calculations of products that are derived from the above geophysical observables, such as Joule heating, energy transfer rates between species, electrical currents, electrical conductivity, ion-neutral collision frequencies between all combinations of species, as well as height-integrations of derived products. 2) Calculation and cross-comparison of collision frequencies and estimates of the effect of using different models of collision frequencies into derived products. 3) Calculation of the uncertainties of derived products based on the uncertainties of the geophysical observables, due to instrument errors or to uncertainties in measurement techniques. 4) Routines for the along-orbit interpolation within gridded datasets of GCMs. 5) Routines for the calculation of the global coverage of an in situ mission in regions of interest and for various conditions of solar and geomagnetic activity. 6) Calculations of the statistical significance of obtaining the primary and derived products throughout an in situ mission’s lifetime. 7) Routines for the visualization of 3D datasets of GCMs and of measurements along orbit. Daedalus MASE code is accompanied by a set of Jupyter Notebooks, incorporating all required theory, references, codes and plotting in a user-friendly environment. Daedalus MASE is developed and maintained at the Department for Electrical and Computer Engineering of the Democritus University of Thrace, with key contributions from several partner institutions.
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| 39. |
- Sarris, Theodoros, et al.
(författare)
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Plasma-neutral interactions in the lower thermosphere-ionosphere : The need for in situ measurements to address focused questions
- 2023
-
Ingår i: Frontiers in Astronomy and Space Sciences. - : Frontiers Media SA. - 2296-987X. ; 9
-
Forskningsöversikt (refereegranskat)abstract
- The lower thermosphere-ionosphere (LTI) is a key transition region between Earth's atmosphere and space. Interactions between ions and neutrals maximize within the LTI and in particular at altitudes from 100 to 200 km, which is the least visited region of the near-Earth environment. The lack of in situ co-temporal and co-spatial measurements of all relevant parameters and their elusiveness to most remote-sensing methods means that the complex interactions between its neutral and charged constituents remain poorly characterized to this date. This lack of measurements, together with the ambiguity in the quantification of key processes in the 100-200 km altitude range affect current modeling efforts to expand atmospheric models upward to include the LTI and limit current space weather prediction capabilities. We present focused questions in the LTI that are related to the complex interactions between its neutral and charged constituents. These questions concern core physical processes that govern the energetics, dynamics, and chemistry of the LTI and need to be addressed as fundamental and long-standing questions in this critically unexplored boundary region. We also outline the range of in situ measurements that are needed to unambiguously quantify key LTI processes within this region, and present elements of an in situ concept based on past proposed mission concepts.
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| 40. |
- Schuettpelz, Eric, et al.
(författare)
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A community-derived classification for extant lycophytes and ferns
- 2016
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Ingår i: Journal of Systematics and Evolution. - : Wiley. - 1674-4918 .- 1759-6831. ; 54:6, s. 563-603
-
Tidskriftsartikel (refereegranskat)abstract
- Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community-based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.
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| 41. |
- Shen, Qian, et al.
(författare)
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The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis
- 2018
-
Ingår i: Molecular Plant. - : Cell Press. - 1674-2052 .- 1752-9867. ; 11:6, s. 776-788
-
Tidskriftsartikel (refereegranskat)abstract
- Artemisia annua, commonly known as sweet wormwood or Qinghao, is a shrub native to China and has long been used for medicinal purposes. A. annua is now cultivated globally as the only natural source of a potent anti-malarial compound, artemisinin. Here, we report a high-quality draft assembly of the 1.74-gigabase genome of A. annua, which is highly heterozygous, rich in repetitive sequences, and contains 63 226 protein-coding genes, one of the largest numbers among the sequenced plant species. We found that, as one of a few sequenced genomes in the Asteraceae, the A. annua genome contains a large number of genes specific to this large angiosperm clade. Notably, the expansion and functional diversification of genes encoding enzymes involved in terpene biosynthesis are consistent with the evolution of the artemisinin biosynthetic pathway. We further revealed by transcriptome profiling that A. annua has evolved the sophisticated transcriptional regulatory networks underlying artemisinin biosynthesis. Based on comprehensive genomic and transcriptomic analyses we generated transgenic A. annua lines producing high levels of artemisinin, which are now ready for large-scale production and thereby will help meet the challenge of increasing global demand of artemisinin.
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| 42. |
- Sidén, Johan, 1975-, et al.
(författare)
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Design of High-Directivity Wideband Microstrip Directional Coupler With Fragment-Type Structure
- 2015
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Ingår i: IEEE transactions on microwave theory and techniques. - 0018-9480 .- 1557-9670. ; 63:12, s. 3962-3970
-
Tidskriftsartikel (refereegranskat)abstract
- A novel design for a microstrip wideband directional coupler is proposedby using fragment-type structures. The use of a fragment-type structuremay provide satisfactory flexibility and excellent performance. For agiven design space, a fragment-type wideband coupler can be designed byfirst gridding the space into fragment cells and then metallizing thefragment cells selected by a multi-objective optimization searchingalgorithm, such as a multi-objective evolutionary algorithm based ondecomposition combined with enhanced genetic operators. Fordemonstration, a 20-dB wideband microstrip directional coupler isdesigned and verified by test. A 45% bandwidth centered at 2 GHz hasbeen measured in terms of maximum variation of 0.5 dB in the 20-dBcoupling level. In the operation band, the designed coupler hasdirectivity above 37 dB, and a maximum directivity of 48 dB at 2 GHz. Inaddition, some technique aspects related to multi-objective optimizationsearching, such as effects of design space, control of coupling level,and efficiency consideration for optimization searching, are furtherdiscussed. Fragment-type structures may also be used to designhigh-performance wideband directional couplers of tight coupling level.
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| 43. |
- Song, Gang, et al.
(författare)
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A zoogeographical boundary between the Palaearctic and Sino-Japanese realms documented by consistent north/south phylogeographical divergences in three woodland birds in eastern China
- 2016
-
Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 43:11, s. 2099-2112
-
Tidskriftsartikel (refereegranskat)abstract
- AimThe location of zoogeographical boundaries in eastern China has long been the subject of debate. To identify any north/south genetic divergence between the Palaearctic and Sino-Japanese realms proposed by previous studies, we conducted a comparative phylogeographical study involving three passerine species with wide latitudinal distributions in eastern China.LocationEastern China.MethodsTwo mitochondrial genes and three nuclear introns were amplified and sequenced. Population structures were analysed using intra-specific phylogeny, tcs networks, AMOVA and structure inferences. We tested for evidence of genetic barriers based on pairwise differences. Lineage divergences, demographic dynamics and gene flow between lineages were estimated using Bayesian methods.ResultsA congruent north/south phylogeographical divergence was identified for three species. A geographical barrier was inferred at c. 40° N in eastern China. The population sizes of the northern and southern lineages have both been stable through the late Pleistocene, while multiple divergences were inferred during the early and middle Pleistocene.Main conclusionsOur results suggest a general phylogeographical break in north-eastern China, coinciding with the Palaearctic/Sino-Japanese boundary. Physical blocking of the Yan Mountains and fragmentation of suitable habitat during glacial stages between the north and south probably acted together to provide long-lasting barrier effects. Our comparative phylogeographical approach demonstrates that the Palaearctic/Sino-Japanese boundary may represent a gene-flow barrier even within widespread species.
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| 44. |
- Sun, Xiao-dong, et al.
(författare)
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Implementing a novel capture and ligation probe-PCR method in mass screen and treatment to support malaria elimination efforts in the China-Myanmar border region
- 2023
-
Ingår i: Malaria Journal. - : BioMed Central (BMC). - 1475-2875. ; 22:1
-
Tidskriftsartikel (refereegranskat)abstract
- BackgroundMass screening and treatment (MSAT) for malaria elimination lacks an ideal diagnostic tool to allow sensitive and affordable test of the target population in the field. This study evaluated whether Capture and Ligation Probe-PCR (CLIP-PCR) could be used in a field MSAT in Laiza City, Myanmar.MethodsOn day 0, two dried blood spots were collected from each participant. On day 1, all samples were screened for Plasmodium in a 20 m(2) laboratory with workbench, a biosafety cabinet, a refrigerator, a benchtop shaking incubator and a qPCR machine, by four technicians using CLIP-PCR with sample pooling, at a health clinic of the Chinese bordering town of Nabang. On day 2, all positives were followed up and treated.ResultsOf 15,038 persons (65% of the total population) screened, 204 (1.36%) were CLIP-PCR positives. Among them, 188, 14, and 2 were infected with Plasmodium vivax, Plasmodium falciparum, and P. vivax/P. falciparum mix, respectively. The testing capacity was 538 persons/day, with a cost of US$0.92 /person. The proportion of submicroscopic infection was 64.7%. All positive individuals received treatment within 72 h after blood collection.ConclusionUsing CLIP-PCR in MSAT in low transmission settings can support the malaria elimination efforts in the China-Myanmar border region.
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| 45. |
- Teng, Lidong, et al.
(författare)
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Thermodynamic investigations of Cr3C2 and reassessment of the Cr-C system
- 2004
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Ingår i: Metallurgical and Materials Transactions. A. - : Springer Science and Business Media LLC. - 1073-5623 .- 1543-1940. ; 35A:12, s. 3673-3680
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Tidskriftsartikel (refereegranskat)abstract
- The Gibbs energies of formation for Cr3C2, Δ fG°Cr3C2, have been obtained from electromotive force (EMF) measurements, in the temperature range 950 to 1150 K, using the following galvanic cells with CaF2 single crystals as the electrolyte: Cr, CrF2 CaF2 CrF2, Cr 3C2, C (950 to 1150 K) Extreme precautions were taken during the experimental measurements to avoid errors. The reliability and reproducibility of the values were confirmed by careful repetition of several of the experiments. The following equation has been obtained by a linear analysis of the EMF results as a function of temperature: ΔfG°Cr3C2(± 1600) = - 58,857 - 22.344T (J·mo1-1) (950 to 1150 K) The generated values are compared with those reported in the literature. The values of the enthalpy of formation were evaluated by using a third-law analysis, and an average value of ΔfH° 298 = -71.7 kJ/mol was obtained. The ground-state energy of the hypothetic end-member compound CrC3 in the bcc structure at 0 K was calculated by using the ab initio method. The experimental results obtained, as well as the results from the ab initio calculations, were employed in a reassessment of the Cr-C system using the CALPHAD approach. A new set of parameters for the bcc phase was evaluated using first-principles calculations.
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| 46. |
- Wang, Chengdong, et al.
(författare)
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The proto-oncogene transcription factor Ets1 regulates neural crest development through Histone Deacetylase 1 to mediate output of bone morphogenetic protein signaling.
- 2015
-
Ingår i: Journal of Biological Chemistry. - 1083-351X. ; 290:36, s. 21925-21938
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Tidskriftsartikel (refereegranskat)abstract
- The neural crest (NC) is a transient, migratory cell population that differentiates into a large variety of tissues including craniofacial cartilage, melanocytes, and peripheral nervous system. NC is initially induced at the border of neural plate and non-neuralectoderm by balanced regulation of multiple signaling pathways, among which an intermediate bone morphogenetic protein (BMP) signaling is essential for NC formation. Ets1, a proto-oncogene playing important roles in tumor invasion, has also been implicated in delamination of NC cells. In this study, we investigated Ets1 function in NC formation using Xenopus. Overexpression of ets1 repressed NC formation through down-regulation of BMP signaling. Moreover, ets1 repressed the BMP-responsive gene id3 that is essential for NC formation. Conversely, overexpression of id3 can partially rescue the phenotype of NC inhibition induced by ectopic ets1. Mechanistically, we found that Ets1 binds to id3 promoter as well as Histone Deacetylase 1 (HDAC1), suggesting that Ets1 recruits HDAC1 to the promoter of id3, thereby inducing Histone deacetylation of the id3 promoter. Thus, our studies indicate that Ets1 regulates NC formation through attenuating BMP signaling epigenetically.
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| 47. |
- Wang, J. H., et al.
(författare)
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Thermodynamic reassessment of the Au-Te system
- 2006
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Ingår i: Journal of Alloys and Compounds. - : Elsevier BV. - 0925-8388 .- 1873-4669. ; 407:1-2, s. 106-111
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Tidskriftsartikel (refereegranskat)abstract
- The Au-Te binary system has been thermodynamically reassessed using the CALPHALD method. The excess Gibbs energy of the liquid phase was formulated with the Redlich-Kister expression and the AuTe2 intermetallic phase was treated as a stoichiometric compound. A set of self-consistent thermodynamic parameters for each phase has been obtained. Good agreement is reached between the calculated and experimental results. Additionally, the standard formation enthalpy and enthalpy of fusion of AuTe2 intermetallic phase have also been calculated.
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| 48. |
- Wang, Jingjing, et al.
(författare)
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Thermodynamic and diffusion kinetic studies of the Fe-Co system
- 2017
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Ingår i: Calphad. - : Elsevier. - 0364-5916 .- 1873-2984. ; 58, s. 82-100
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Tidskriftsartikel (refereegranskat)abstract
- The phase equilibria, thermodynamic properties and diffusion mobilities of the Fe-Co system were carefully assessed through the CALPHAD methods. As an indispensable tool, the first-principles calculations were carried out to study the magnetic moments and the enthalpies of mixing of the bcc_A2, bcc_B2, fcc_A1 and hcp_A3 phases as well as the point defect types of the bcc_B2 phase. In order to verify the heat capacities reported in the literature, new measurements were conducted in a high-temperature calorimetric apparatus using the three-dimensional calorimetric method. Because of the revision of the thermodynamic parameters in the present work, the diffusion mobilities for the fcc_Al phase were reassessed. The diffusion mobilities for the bcc_A2 phase were established for the first time based on the experimental diffusion coefficients. For the low temperature bcc_B2 phase, the diffusion couple experiments conducted in the present work show that the diffusion process is sluggish and the interdiffusion coefficients are difficult to determine. Therefore the tracer diffusivities of Co and Fe in the Fe-Co alloys were used to assess the diffusion mobilities for the bcc_B2 phase, while the composition-distance profile of one diffusion couple was served as a validation of its diffusion mobilities.
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| 49. |
- Wang, Lu, et al.
(författare)
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Design of Chipless RFID Tag by Using Miniaturized Open-Loop Resonators
- 2018
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Ingår i: IEEE Transactions on Antennas and Propagation. - 0018-926X .- 1558-2221. ; 66:2, s. 618-626
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, an open-loop resonator with fragment-loading structure is used for the first time in the design of radar cross section-based chipless radio-frequency identification (RFID) tag. By optimizing the distribution of fragment patches in an open loop, a microstrip open-loop resonator can be miniaturized so that the data capacity of the chipless RFID tag designed using such a miniaturized loop resonator can be significantly increased. Moreover, the resonant frequency of the fragment-loaded resonator can be adjusted conveniently by removing or disconnecting some fragment patches, which provides great flexibility for data encoding of the chipless RFID tag. The proposed chipless RFID tag with miniaturized open-loop resonators is designed and tested and can acquire 3.56 bits per resonator and a coding density of approximately 745.1bits/λg 2. Several experimental results validate the proposed design as well as its implementation in a realistic environment.
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| 50. |
- Wang, Lu, et al.
(författare)
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High-performance tight coupling microstrip directional coupler with fragment-type compensated structure
- 2017
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Ingår i: IET Microwaves, Antennas & Propagation. - : Institution of Engineering and Technology (IET). - 1751-8725 .- 1751-8733. ; 11:7, s. 1057-1063
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Tidskriftsartikel (refereegranskat)abstract
- In this study, a design scheme for high-performance tight coupling microstrip coupler is proposed by adding a fragment-type compensated structure between two loosely coupled lines. Owing to its flexibility and adaptability, the fragment-type compensated structure can not only provide a quarter-wavelength phase shift for coupling enhancement, but also compensate the difference in the phase velocities of the even- and odd-modes for high directivity. Design of the fragment-type compensated structure can be implemented by multi-objective optimisation searching with several design objectives characterising tight coupling couplers. A high-efficiency optimisation searching strategy by using two-dimensional median filtering operator is employed to improve the efficiency of multi-objective optimisation. For demonstration, a high-performance 3-dB tight coupling directional coupler operating at 2 GHz is designed. The measurement data demonstrates a maximum directivity of 47 dB, above 25 dB directivity in a 21.5% bandwidth, a maximum variation of 0.3 dB in the coupling level and a maximum power division ratio of 0.6 dB, which indicate the overall performance better than the previously reported 3-dB couplers. In addition, a simplified theoretical analysis of the proposed coupler and full-wave simulated results are provided for better understanding of the fragment-type compensated structure.
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