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- 2019
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Tidskriftsartikel (refereegranskat)
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| 5. |
- Couch, Fergus J., et al.
(författare)
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Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
- 2016
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 7:11375, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- Common variants in 94 loci have been associated with breast cancer including 15 loci with genome-wide significant associations (P<5 x 10(-8)) with oestrogen receptor (ER)-negative breast cancer and BRCA1-associated breast cancer risk. In this study, to identify new ER-negative susceptibility loci, we performed a meta-analysis of 11 genome-wide association studies (GWAS) consisting of 4,939 ER-negative cases and 14,352 controls, combined with 7,333 ER-negative cases and 42,468 controls and 15,252 BRCA1 mutation carriers genotyped on the iCOGS array. We identify four previously unidentified loci including two loci at 13q22 near KLF5, a 2p23.2 locus near WDR43 and a 2q33 locus near PPIL3 that display genome-wide significant associations with ER-negative breast cancer. In addition, 19 known breast cancer risk loci have genome-wide significant associations and 40 had moderate associations (P<0.05) with ER-negative disease. Using functional and eQTL studies we implicate TRMT61B and WDR43 at 2p23.2 and PPIL3 at 2q33 in ER-negative breast cancer aetiology. All ER-negative loci combined account for similar to 11% of familial relative risk for ER-negative disease and may contribute to improved ER-negative and BRCA1 breast cancer risk prediction.
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| 6. |
- Hollestelle, Antoinette, et al.
(författare)
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No clinical utility of KRAS variant rs61764370 for ovarian or breast cancer
- 2016
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Ingår i: Gynecologic Oncology. - : Elsevier BV. - 0090-8258 .- 1095-6859. ; 141:2, s. 386-401
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Tidskriftsartikel (refereegranskat)abstract
- Objective Clinical genetic testing is commercially available for rs61764370, an inherited variant residing in a KRAS 3′ UTR microRNA binding site, based on suggested associations with increased ovarian and breast cancer risk as well as with survival time. However, prior studies, emphasizing particular subgroups, were relatively small. Therefore, we comprehensively evaluated ovarian and breast cancer risks as well as clinical outcome associated with rs61764370. Methods Centralized genotyping and analysis were performed for 140,012 women enrolled in the Ovarian Cancer Association Consortium (15,357 ovarian cancer patients; 30,816 controls), the Breast Cancer Association Consortium (33,530 breast cancer patients; 37,640 controls), and the Consortium of Modifiers of BRCA1 and BRCA2 (14,765 BRCA1 and 7904 BRCA2 mutation carriers). Results We found no association with risk of ovarian cancer (OR = 0.99, 95% CI 0.94-1.04, p = 0.74) or breast cancer (OR = 0.98, 95% CI 0.94-1.01, p = 0.19) and results were consistent among mutation carriers (BRCA1, ovarian cancer HR = 1.09, 95% CI 0.97-1.23, p = 0.14, breast cancer HR = 1.04, 95% CI 0.97-1.12, p = 0.27; BRCA2, ovarian cancer HR = 0.89, 95% CI 0.71-1.13, p = 0.34, breast cancer HR = 1.06, 95% CI 0.94-1.19, p = 0.35). Null results were also obtained for associations with overall survival following ovarian cancer (HR = 0.94, 95% CI 0.83-1.07, p = 0.38), breast cancer (HR = 0.96, 95% CI 0.87-1.06, p = 0.38), and all other previously-reported associations. Conclusions rs61764370 is not associated with risk of ovarian or breast cancer nor with clinical outcome for patients with these cancers. Therefore, genotyping this variant has no clinical utility related to the prediction or management of these cancers.
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| 7. |
- Lawrenson, Kate, et al.
(författare)
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Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk.
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| 8. |
- Lu, Yingchang, et al.
(författare)
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A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk.
- 2018
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Ingår i: Cancer Research. - 0008-5472 .- 1538-7445. ; 78:18, s. 5419-5430
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Tidskriftsartikel (refereegranskat)abstract
- .AbstractLarge-scale genome-wide association studies (GWAS) have identified approximately 35 loci associated with epithelial ovarian cancer (EOC) risk. The majority of GWAS-identified disease susceptibility variants are located in noncoding regions, and causal genes underlying these associations remain largely unknown. Here, we performed a transcriptome-wide association study to search for novel genetic loci and plausible causal genes at known GWAS loci. We used RNA sequencing data (68 normal ovarian tissue samples from 68 individuals and 6,124 cross-tissue samples from 369 individuals) and high-density genotyping data from European descendants of the Genotype-Tissue Expression (GTEx V6) project to build ovarian and cross-tissue models of genetically regulated expression using elastic net methods. We evaluated 17,121 genes for their cis-predicted gene expression in relation to EOC risk using summary statistics data from GWAS of 97,898 women, including 29,396 EOC cases. With a Bonferroni-corrected significance level of P < 2.2 × 10−6, we identified 35 genes, including FZD4 at 11q14.2 (Z = 5.08, P = 3.83 × 10−7, the cross-tissue model; 1 Mb away from any GWAS-identified EOC risk variant), a potential novel locus for EOC risk. All other 34 significantly associated genes were located within 1 Mb of known GWAS-identified loci, including 23 genes at 6 loci not previously linked to EOC risk. Upon conditioning on nearby known EOC GWAS-identified variants, the associations for 31 genes disappeared and three genes remained (P < 1.47 × 10−3). These data identify one novel locus (FZD4) and 34 genes at 13 known EOC risk loci associated with EOC risk, providing new insights into EOC carcinogenesis.Significance: Transcriptomic analysis of a large cohort confirms earlier GWAS loci and reveals FZD4 as a novel locus associated with EOC risk. Cancer Res; 78(18); 5419–30. ©2018 AACR.
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| 9. |
- Machiela, Mitchell J., et al.
(författare)
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Characterization of Large Structural Genetic Mosaicism in Human Autosomes
- 2015
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 96:3, s. 487-497
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Tidskriftsartikel (refereegranskat)abstract
- Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 x 3 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.
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| 10. |
- Muus, Christoph, et al.
(författare)
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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
- 2021
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:3, s. 546-559
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Tidskriftsartikel (refereegranskat)abstract
- Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2(+)TMPRSS2(+) cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention. An integrated analysis of over 100 single-cell and single-nucleus transcriptomics studies illustrates severe acute respiratory syndrome coronavirus 2 viral entry gene coexpression patterns across different human tissues, and shows association of age, smoking status and sex with viral entry gene expression in respiratory cell populations.
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| 11. |
- Turro, Ernest, et al.
(författare)
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Whole-genome sequencing of patients with rare diseases in a national health system.
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 583:7814, s. 96-102
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Tidskriftsartikel (refereegranskat)abstract
- Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and causative genes for more than half such disorders remain to be discovered1. Here we used whole-genome sequencing (WGS) in a national health system to streamline diagnosis and to discover unknown aetiological variants in the coding and non-coding regions of the genome. We generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065extensively phenotypedparticipants. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed to be aetiological. By generating WGS data ofUK Biobankparticipants2, we found that rare alleles can explain the presence of some individuals in the tails of a quantitative trait for red blood cells. Finally, we identified four novel non-coding variants that cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.
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| 12. |
- Zeng, Chenjie, et al.
(författare)
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Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus
- 2016
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Ingår i: Breast Cancer Research. - : Springer Science and Business Media LLC. - 1465-5411 .- 1465-542X. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- Background: Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk. Method: We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation. Results: Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06-1.12; P = 3 x 10(-9)), rs805510 (OR = 1.08, 95 % CI = 1.04-1.12, P = 2 x 10(-5)), and rs1871152 (OR = 1.04, 95 % CI = 1.02-1.06; P = 2 x 10(-4)) identified in the general populations, and rs113824616 (P = 7 x 10(-5)) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P < 0.05 in East Asians, but none of the associations were statistically significant in African descendants. Multiple candidate functional variants are located in putative enhancer sequences. Chromatin interaction data suggested that PTHLH was the likely target gene of these enhancers. Of the six variants with the strongest evidence of potential functionality, rs11049453 was statistically significantly associated with the expression of PTHLH and its nearby gene CCDC91 at P < 0.05. Conclusion: This study identified four independent association signals at 12p11 and revealed potentially functional variants, providing additional insights into the underlying biological mechanism(s) for the association observed between variants at 12p11 and breast cancer risk.
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| 13. |
- Antoniou, Antonis C., et al.
(författare)
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A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with hormone receptor-negative breast cancer in the general population
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 42:10, s. 885-892
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Tidskriftsartikel (refereegranskat)abstract
- Germline BRCA1 mutations predispose to breast cancer. To identify genetic modifiers of this risk, we performed a genome-wide association study in 1,193 individuals with BRCA1 mutations who were diagnosed with invasive breast cancer under age 40 and 1,190 BRCA1 carriers without breast cancer diagnosis over age 35. We took forward 96 SNPs for replication in another 5,986 BRCA1 carriers (2,974 individuals with breast cancer and 3,012 unaffected individuals). Five SNPs on 19p13 were associated with breast cancer risk (P-trend = 2.3 x 10(-9) to Ptrend = 3.9 x 10(-7)), two of which showed independent associations (rs8170, hazard ratio (HR) = 1.26, 95% CI 1.17-1.35; rs2363956 HR = 0.84, 95% CI 0.80-0.89). Genotyping these SNPs in 6,800 population-based breast cancer cases and 6,613 controls identified a similar association with estrogen receptor-negative breast cancer (rs2363956 per-allele odds ratio (OR) = 0.83, 95% CI 0.75-0.92, P-trend = 0.0003) and an association with estrogen receptor-positive disease in the opposite direction (OR = 1.07, 95% CI 1.01-1.14, P-trend = 0.016). The five SNPs were also associated with triple-negative breast cancer in a separate study of 2,301 triple-negative cases and 3,949 controls (Ptrend = 1 x 10(-7) to Ptrend = 8 x 10(-5); rs2363956 per-allele OR = 0.80, 95% CI 0.74-0.87, P-trend = 1.1 x 10(-7)).
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| 14. |
- Bakhit, Babak, 1983-, et al.
(författare)
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Age hardening in superhard ZrB2-rich Zr1-xTaxBy thin films
- 2021
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Ingår i: Scripta Materialia. - : Elsevier. - 1359-6462 .- 1872-8456. ; 191, s. 120-125
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Tidskriftsartikel (refereegranskat)abstract
- We recently showed that sputter-deposited Zr1-xTaxBy thin films have hexagonal AlB2-type columnar nanostructure in which column boundaries are B-rich for x < 0.2, while Ta-rich for x ≥ 0.2. As-deposited layers with x ≥ 0.2 exhibit higher hardness and, simultaneously, enhanced toughness. Here, we study the mechanical properties of ZrB2.4, Zr0.8Ta0.2B1.8, and Zr0.7Ta0.3B1.5 films annealed in Ar atmosphere as a function of annealing temperature Ta up to 1200 °C. In-situ and ex-situ nanoindentation analyses reveal that all films undergo age hardening up to Ta = 800 °C, with the highest hardness achieved for Zr0.8Ta0.2B1.8 (45.5±1.0 GPa). The age hardening, which occurs without any phase separation or decomposition, can be explained by point-defect recovery that enhances chemical bond density. Although hardness decreases at Ta > 800 °C due mainly to recrystallization, column coarsening, and planar defect annihilation, all layers show hardness values above 34 GPa over the entire Ta range.
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| 15. |
- Bolton, Kelly L., et al.
(författare)
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Association Between BRCA1 and BRCA2 Mutations and Survival in Women With Invasive Epithelial Ovarian Cancer
- 2012
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Ingår i: JAMA: The Journal of the American Medical Association. - : American Medical Association (AMA). - 1538-3598. ; 307:4, s. 382-390
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Tidskriftsartikel (refereegranskat)abstract
- Context Approximately 10% of women with invasive epithelial ovarian cancer (EOC) carry deleterious germline mutations in BRCA1 or BRCA2. A recent article suggested that BRCA2-related EOC was associated with an improved prognosis, but the effect of BRCA1 remains unclear. Objective To characterize the survival of BRCA carriers with EOC compared with noncarriers and to determine whether BRCA1 and BRCA2 carriers show similar survival patterns. Design, Setting, and Participants A pooled analysis of 26 observational studies on the survival of women with ovarian cancer, which included data from 1213 EOC cases with pathogenic germline mutations in BRCA1 (n=909) or BRCA2 (n=304) and from 2666 noncarriers recruited and followed up at variable times between 1987 and 2010 (the median year of diagnosis was 1998). Main Outcome Measure Five-year overall mortality. Results The 5-year overall survival was 36% (95% CI, 34%-38%) for noncarriers, 44% (95% CI, 40%-48%) for BRCA1 carriers, and 52% (95% CI, 46%-58%) for BRCA2 carriers. After adjusting for study and year of diagnosis, BRCA1 and BRCA2 mutation carriers showed a more favorable survival than noncarriers (for BRCA1: hazard ratio [HR], 0.78; 95% CI, 0.68-0.89; P<.001; and for BRCA2: HR, 0.61; 95% CI, 0.50-0.76; P<.001). These survival differences remained after additional adjustment for stage, grade, histology, and age at diagnosis (for BRCA1: HR, 0.73; 95% CI, 0.64-0.84; P<.001; and for BRCA2: HR, 0.49; 95% CI, 0.39-0.61; P<.001). The BRCA1 HR estimate was significantly different from the HR estimated in the adjusted model (P for heterogeneity=.003). Conclusion Among patients with invasive EOC, having a germline mutation in BRCA1 or BRCA2 was associated with improved 5-year overall survival. BRCA2 carriers had the best prognosis. JAMA. 2012;307(4):382-390
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| 16. |
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| 17. |
- Couthouis, Julien, et al.
(författare)
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A yeast functional screen predicts new candidate ALS disease genes
- 2011
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 108:52, s. 20881-20890
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Tidskriftsartikel (refereegranskat)abstract
- Amyotrophic lateral sclerosis (ALS) is a devastating and universally fatal neurodegenerative disease. Mutations in two related RNA-binding proteins, TDP-43 and FUS, that harbor prion-like domains, cause some forms of ALS. There are at least 213 human proteins harboring RNA recognition motifs, including FUS and TDP-43, raising the possibility that additional RNA-binding proteins might contribute to ALS pathogenesis. We performed a systematic survey of these proteins to find additional candidates similar to TDP-43 and FUS, followed by bioinformatics to predict prion-like domains in a subset of them. We sequenced one of the segenes, TAF15, in patients with ALS and identified missense variants, which were absent in a large number of healthy controls. These disease-associated variants of TAF15 caused formation of cytoplasmic foci when expressed in primary cultures of spinal cord neurons. Very similar to TDP-43 and FUS, TAF15 aggregated in vitro and conferred neurodegeneration in Drosophila, with the ALS-linked variants having amore severe effect than wild type. Immunohistochemistry of postmortem spinal cord tissue revealed mislocalization of TAF15 in motor neurons of patients with ALS. We propose that aggregation-prone RNA-binding proteins might contribute very broadly to ALS pathogenesis and the genes identified in our yeast functional screen, coupled with prion-like domain prediction analysis, now provide a powerful resource to facilitate ALS disease gene discovery.
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| 18. |
- Ding, Yuan C, et al.
(författare)
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A nonsynonymous polymorphism in IRS1 modifies risk of developing breast and ovarian cancers in BRCA1 and ovarian cancer in BRCA2 mutation carriers
- 2012
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Ingår i: Cancer Epidemiology, Biomarkers and Prevention. - : American Association for Cancer Research. - 1055-9965 .- 1538-7755. ; 21:8, s. 1362-1370
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: We previously reported significant associations between genetic variants in insulin receptor substrate 1 (IRS1) and breast cancer risk in women carrying BRCA1 mutations. The objectives of this study were to investigate whether the IRS1 variants modified ovarian cancer risk and were associated with breast cancer risk in a larger cohort of BRCA1 and BRCA2 mutation carriers.METHODS: IRS1 rs1801123, rs1330645, and rs1801278 were genotyped in samples from 36 centers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Data were analyzed by a retrospective cohort approach modeling the associations with breast and ovarian cancer risks simultaneously. Analyses were stratified by BRCA1 and BRCA2 status and mutation class in BRCA1 carriers.RESULTS: Rs1801278 (Gly972Arg) was associated with ovarian cancer risk for both BRCA1 (HR, 1.43; 95% confidence interval (CI), 1.06-1.92; P = 0.019) and BRCA2 mutation carriers (HR, 2.21; 95% CI, 1.39-3.52, P = 0.0008). For BRCA1 mutation carriers, the breast cancer risk was higher in carriers with class II mutations than class I mutations (class II HR, 1.86; 95% CI, 1.28-2.70; class I HR, 0.86; 95%CI, 0.69-1.09; P(difference), 0.0006). Rs13306465 was associated with ovarian cancer risk in BRCA1 class II mutation carriers (HR, 2.42; P = 0.03).CONCLUSION: The IRS1 Gly972Arg single-nucleotide polymorphism, which affects insulin-like growth factor and insulin signaling, modifies ovarian cancer risk in BRCA1 and BRCA2 mutation carriers and breast cancer risk in BRCA1 class II mutation carriers.Impact: These findings may prove useful for risk prediction for breast and ovarian cancers in BRCA1 and BRCA2 mutation carriers.
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| 19. |
- Dyrek, Achrène, et al.
(författare)
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SO2, silicate clouds, but no CH4 detected in a warm Neptune
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625, s. 51-54
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Tidskriftsartikel (refereegranskat)abstract
- WASP-107b is a warm (approximately 740 K) transiting planet with a Neptune-like mass of roughly 30.5 M⊕ and Jupiter-like radius of about 0.94 RJ (refs. 1,2), whose extended atmosphere is eroding3. Previous observations showed evidence for water vapour and a thick, high-altitude condensate layer in the atmosphere of WASP-107b (refs. 4,5). Recently, photochemically produced sulfur dioxide (SO2) was detected in the atmosphere of a hot (about 1,200 K) Saturn-mass planet from transmission spectroscopy near 4.05 μm (refs. 6,7), but for temperatures below about 1,000 K, sulfur is predicted to preferably form sulfur allotropes instead of SO2 (refs. 8,9,10). Here we report the 9σ detection of two fundamental vibration bands of SO2, at 7.35 μm and 8.69 μm, in the transmission spectrum of WASP-107b using the Mid-Infrared Instrument (MIRI) of JWST. This discovery establishes WASP-107b as the second irradiated exoplanet with confirmed photochemistry, extending the temperature range of exoplanets exhibiting detected photochemistry from about 1,200 K down to about 740 K. Furthermore, our spectral analysis reveals the presence of silicate clouds, which are strongly favoured (around 7σ) over simpler cloud set-ups. Furthermore, water is detected (around 12σ) but methane is not. These findings provide evidence of disequilibrium chemistry and indicate a dynamically active atmosphere with a super-solar metallicity.
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| 20. |
- Edström, Daniel, et al.
(författare)
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Effects of incident N atom kinetic energy on TiN/TiN(001) film growth dynamics: A molecular dynamics investigation
- 2017
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Ingår i: Journal of Applied Physics. - : AMER INST PHYSICS. - 0021-8979 .- 1089-7550. ; 121:2
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale classical molecular dynamics simulations of epitaxial TiN/TiN(001) thin film growth at 1200 K, a temperature within the optimal range for epitaxial TiN growth, with an incident N-to-Ti flux ratio of four, are carried out using incident N energies E-N = 2 and 10 eV and incident Ti energy E-Ti = 2 eV. To further highlight the effect of E-N, we grow a bilayer film with E-N = 2 eV initially and then switch to E-N = 10 eV. As-deposited layers are analyzed as a function of composition, island-size distribution, island-edge orientation, and vacancy formation. Results show that growth with E-N = 2 eV results in films that are globally overstoichiometric with islands bounded by N-terminated polar 110 edges, whereas films grown with E-N = 10 eV are flatter and closer to stoichiometric. However, E-N = 10 eV layers exhibit local N deficiency leading to the formation of isolated 111-oriented islands. Films grown by changing the incident energy from 2 to 10 eV during growth are more compact than those grown entirely with E-N = 2 eV and exhibit greatly reduced concentrations of upper-layer adatoms, admolecules, and small clusters. Islands with 110 edges formed during growth with E-N = 2 eV transform to islands with 100 edges as E-N is switched to 10 eV. Published by AIP Publishing.
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| 21. |
- Edström, Daniel, et al.
(författare)
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Elastic properties and plastic deformation of TiC- and VC-based alloys
- 2018
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Ingår i: Acta Materialia. - : PERGAMON-ELSEVIER SCIENCE LTD. - 1359-6454 .- 1873-2453. ; 144, s. 376-385
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Tidskriftsartikel (refereegranskat)abstract
- Transition-metal (TM) carbides are an important class of hard, protective coating materials; however, their brittleness often limits potential applications. We use density functional theory to investigate the possibility of improving ductility by forming pseudobinary cubic (MMC)-M-1-C-2 alloys, for which M-1 = Ti or V and M-2 = W or Mo. The alloying elements are chosen based on previous results showing improved ductility of the corresponding pseudobinary nitride alloys with respect to their parent compounds. While commonly-used empirical criteria do not indicate enhanced ductility in the carbide alloys, calculated stress/strain curves along known slip systems, supported by electronic structure analyses, indicate ductile behavior for VMoC. As VMoC layers are sheared along the 1 (1) over bar0 direction on {111} planes, the stress initially increases linearly up to a yield point where the accumulated stress is partially dissipated. With further increase in strain, the stress increases again until fracture occurs. A similar mechanical behavior is observed for the corresponding TM nitride VMoN, known to be a ductile ceramic material [1]. Thus, our results show that VMoC is a TM carbide alloy which may be both hard and ductile, i.e. tough. (C) 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
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| 22. |
- Edström, Daniel, et al.
(författare)
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Large-scale molecular dynamics simulations of TiN/TiN(001) epitaxial film growth
- 2016
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Ingår i: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : AMER INST PHYSICS. - 0734-2101 .- 1520-8559. ; 34:4, s. 041509-1-041509-9
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale classical molecular dynamics simulations of epitaxial TiN/TiN(001) thin film growth at 1200K are carried out using incident flux ratios N/Ti -1, 2, and 4. The films are analyzed as a function of composition, island size distribution, island edge orientation, and vacancy formation. Results show that N/Ti-1 films are globally understoichiometric with dispersed Ti-rich surface regions which serve as traps to nucleate 111-oriented islands, leading to local epitaxial breakdown. Films grown with N/Ti=2 are approximately stoichiometric and the growth mode is closer to layer-by-layer, while N/Ti-4 films are stoichiometric with N-rich surfaces. As N/Ti is increased from 1 to 4, island edges are increasingly polar, i. e., 110-oriented, and N-terminated to accommodate the excess N flux, some of which is lost by reflection of incident N atoms. N vacancies are produced in the surface layer during film deposition with N/Ti-1 due to the formation and subsequent desorption of N-2 molecules composed of a N adatom and a N surface atom, as well as itinerant Ti adatoms pulling up N surface atoms. The N vacancy concentration is significantly reduced as N/Ti is increased to 2; with N/Ti-4, Ti vacancies dominate. Overall, our results show that an insufficient N/Ti ratio leads to surface roughening via nucleation of small dispersed 111 islands, whereas high N/Ti ratios result in surface roughening due to more rapid upper-layer nucleation and mound formation. The growth mode of N/Ti-2 films, which have smoother surfaces, is closer to layer-by-layer. (C) 2016 American Vacuum Society.
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| 23. |
- Edström, Daniel, 1986-, et al.
(författare)
-
Mechanical properties of VMoNO as a function of oxygen concentration : Toward development of hard and tough refractory oxynitrides
- 2019
-
Ingår i: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : American Institute of Physics (AIP). - 0734-2101 .- 1520-8559. ; 37:6
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Tidskriftsartikel (refereegranskat)abstract
- Improved toughness is a central goal in the development of wear-resistant refractory ceramic coatings. Extensive theoretical and experimental research has revealed that NaCl-structure VMoN alloys exhibit surprisingly high ductility combined with high hardness and toughness. However, during operation, protective coatings inevitably oxidize, a problem that may compromise material properties and performance. Here, the authors explore the role of oxidation in altering VMoN properties. Density functional theory and theoretical intrinsic hardness models are used to investigate the mechanical behavior of cubic V0.5Mo0.5N1-xOx solid solutions as a function of the oxygen concentration x. Elastic constant and intrinsic hardness calculations show that oxidation does not degrade the mechanical properties of V0.5Mo0.5N. Electronic structure analyses indicate that the presence of oxygen reduces the covalent bond character, which slightly lowers the alloy strength and intrinsic hardness. Nevertheless, the character of metallic d-d states, which are crucial for allowing plastic deformation and enhancing toughness, remains unaffected. Overall, the authors' results suggest that VMoNO oxynitrides, with oxygen concentrations as high as 50%, possess high intrinsic hardness, while still being ductile. Published by the AVS.
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| 24. |
- Edström, Daniel, et al.
(författare)
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The dynamics of TiNx (x = 1 – 3) admolecule interlayer and intralayer transport on TiN/TiN(001) islands
- 2015
-
Ingår i: Thin Solid Films. - : Elsevier. - 0040-6090 .- 1879-2731. ; 589, s. 133-144
-
Tidskriftsartikel (refereegranskat)abstract
- It has been shown both experimentally and by density functional theory calculations that the primary diffusing species during the epitaxial growth of TiN/TiN(001) are Ti and N adatoms together with TiNx complexes (x = 1, 2, 3), in which the dominant N-containing admolecule species depends upon the incident N/Ti flux ratio. Here, we employ classical molecular dynamics (CMD) simulations to probe the dynamics of TiNx (x = 1–3) admolecules on 8 × 8 atom square, single-atom-high TiN islands on TiN(001), as well as pathways for descent over island edges. The simulations are carried out at 1000 K, a reasonable epitaxial growth temperature. We find that despite their lower mobility on infinite TiN(001) terraces, both TiN and TiN2 admolecules funnel toward descending steps and are incorporated into island edges more rapidly than Ti adatoms. On islands, TiN diffuses primarily via concerted translations, but rotation is the preferred diffusion mechanism on infinite terraces. TiN2 migration is initiated primarily by rotation about one of the N admolecule atoms anchored at an epitaxial site. TiN admolecules descend from islands by direct hopping over edges and by edge exchange reactions, while TiN2 trimers descend exclusively by hopping. In contrast, TiN3 admolecules are essentially stationary and serve as initiators for local island growth. Ti adatoms are the fastest diffusing species on infinite TiN(001) terraces, but on small TiN/TiN(001) islands, TiN dimers provide more efficient mass transport. The overall results reveal the effect of the N/Ti precursor flux ratio on TiN(001) surface morphological evolution and growth modes.
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| 25. |
- Edström, Daniel, et al.
(författare)
-
Ti and N adatom descent pathways to the terrace from atop two-dimensional TiN/TiN(001) islands
- 2014
-
Ingår i: Thin Solid Films. - : Elsevier. - 0040-6090 .- 1879-2731. ; 558, s. 37-46
-
Tidskriftsartikel (refereegranskat)abstract
- We use classical molecular dynamics and the modified embedded atom method to determine residence times and descent pathways of Ti and N adatoms on square, single-atom-high, TiN islands on TiN(001). Simulations are carried out at 1000 K, which is within the optimal range for TiN(001) epitaxial growth. Results show that the frequency of descent events, and overall adatom residence times, depend strongly on both the TiN(001) diffusion barrier for each species as well as the adatom island-edge location immediately prior to descent. Ti adatoms, with a low diffusion barrier, rapidly move toward the island periphery, via funneling, where they diffuse along upper island edges. The primary descent mechanism for Ti adatoms is via push-out/exchange with Ti island-edge atoms, a process in which the adatom replaces an island edge atom by moving down while pushing the edge atom out onto the terrace to occupy an epitaxial position along the island edge. Double push-out events are also observed for Ti adatoms descending at N corner positions. N adatoms, with a considerably higher diffusion barrier on TiN(001), require much longer times to reach island edges and, consequently, have significantly longer residence times. N adatoms are found to descend onto the terrace by direct hopping over island edges and corner atoms, as well as by concerted push-out/exchange with N atoms adjacent to Ti corners. For both adspecies, we also observe several complex adatom/island interactions, before and after descent onto the terrace, including two instances of Ti islandatom ascent onto the island surface.
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| 26. |
- Edström, Daniel, 1986-, et al.
(författare)
-
TiN film growth on misoriented TiN grains with simultaneous low-energy bombardment : Restructuring leading to epitaxy
- 2019
-
Ingår i: Thin Solid Films. - : Elsevier. - 0040-6090 .- 1879-2731. ; 688
-
Tidskriftsartikel (refereegranskat)abstract
- We perform large-scale molecular dynamics simulations of TiN deposition at 1200 K on TiN substrates consisting of under-stoichiometric (N/Ti = 0.86) misoriented grains. The energy of incoming Ti atoms is 2 eV and that of incoming N atoms is 10 eV. The simulations show that misoriented grains are reoriented during the early stages of growth, after which the film grows 001 epitaxially and is nearly stoichiometric. The grain reorientation coincides with an increase in film N/Ti ratio. As the grains reorient, additional nitrogen can no longer be accommodated, and the film composition becomes stoichiometric as the overlayer grows epitaxially.
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| 27. |
- Greene, George W., et al.
(författare)
-
Anisotropic dynamic changes in the pore network structure, fluid diffusion and fluid flow in articular cartilage under compression
- 2010
-
Ingår i: Biomaterials. - : Elsevier BV. - 1878-5905 .- 0142-9612. ; 31:12, s. 3117-3128
-
Tidskriftsartikel (refereegranskat)abstract
- A compression cell designed to fit inside an NMR spectrometer was used to investigate the in situ mechanical strain response, structural changes to the internal pore structure, and the diffusion and flow of interstitial water in full-thickness cartilage samples as it was deforming dynamically under a constant compressive load (pressure). We distinguish between the hydrostatic pressure acting on the interstitial fluid and the pore pressure acting on the cartilage fibril network. Our results show that properties related to the pore matrix microstructure such as diffusion and hydraulic conductivity are strongly influenced by the hydrostatic pressure in the interstitial fluid of the dynamically deforming cartilage which differ significantly from the properties measured under static i.e. equilibrium loading conditions (when the hydrostatic pressure has relaxed back to zero). The magnitude of the hydrostatic fluid pressure also appears to affect the way cartilage's pore matrix changes during deformation with implications for the diffusion and flow-driven fluid transport through the deforming pore matrix. We also show strong evidence for a highly anisotropic pore structure and deformational dynamics that allows cartilage to deform without significantly altering the axial porosity of the matrix even at very large strains. The insensitivity of the axial porosity to compressive strain may be playing a critical function in directing the flow of pressurized interstitial fluid in the compressed cartilage to the surface, to support the load, and provide a protective interfacial fluid film that 'weeps' out from the deforming tissue and thereby enhances the (elasto)hydrodynamic efficacy of sliding joints. Our results appear to show a close synergy between the structure of cartilage and both the hydrodynamic and boundary lubrication mechanisms. (C) 2010 Elsevier Ltd. All rights reserved.
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| 28. |
- Greene, George W., et al.
(författare)
-
Changes in pore morphology and fluid transport in compressed articular cartilage and the implications for joint lubrication
- 2008
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Ingår i: Biomaterials. - : Elsevier BV. - 1878-5905 .- 0142-9612. ; 29:33, s. 4455-4462
-
Tidskriftsartikel (refereegranskat)abstract
- Cartilage sections were cut from the middle zone of pig knee articular cartilage and attached to substrates in two different kinds of newly designed 'pressure cells', one for fluorescence the other for NMR measurements, The fluorescence cell was filled with buffer solution containing fluorescently marked 70 kDa dextran which was allowed to diffuse into the cartilage pores. A second glass surface was then pressed down onto the thin cartilage sample under different loads (pressures), and the resulting compression (strain) and change in pore volume were measured as a function of time, simultaneously with measurements of the lateral diffusion and flow pattern of the dextran molecules using Fluorescence Recovery After Photobleaching (FRAP). Complementary experiments were made on the normal diffusion coefficients of pure electrolyte solutions (no dextran) in thicker cartilage sections with pulse-gradient NMR using a new pressure cell suitable for such measurements. Taken together our results show that the highly anisotropic structure of cartilage has a strong effect on the way fluid diffuses laterally and normally at different stages of compression. Our results also show how geometric constraints on a cartilage network and trapped high MW polymer such as HA during normal compressions are likely to affect both the normal and the lateral mobilities of polyelectrolytes and water. (C) 2008 Elsevier Ltd. All rights reserved.
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| 29. |
- Greene, George W., et al.
(författare)
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Hyaluronic acid-collagen network interactions during the dynamic compression and recovery of cartilage
- 2012
-
Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-6848 .- 1744-683X. ; 8:38, s. 9906-9914
-
Tidskriftsartikel (refereegranskat)abstract
- A compression cell designed to fit inside an NMR spectrometer was used to investigate (i) the in situ dynamic strain response and structural changes of the internal pore network, and (ii) the diffusion and flow of interstitial water, in full thickness cartilage samples as they were mechanically deformed under a constant compressive load (pressure) and then allowed to recover (swell again) when the load was removed. Selective enzymatic digestion of the collagen fibril network and the glycopolysaccharide hyaluronic acid (HA) was performed to mimic some of the structural and compositional changes associated with osteoarthritis. Digestion of collagen gave rise to mechanical 'dynamic softening' and-perhaps more importantly-nearly complete loss in the ability to recover through swelling, both effects due to the disruption of the hierarchical structure and fibril interconnectivity in the collagen network which adversely affects its ability to deform reversibly and to properly regulate the pressurization and resulting rate and direction of interstitial fluid flow. In contrast, digestion of HA inside the collagen pore network caused the cartilage to 'dynamically stiffen' which is attributed to the decrease in the osmotic (entropic) pressure of the digested HA molecules confined in the cartilage pores that causes the network to contract and thereby become less permeable to flow. These digestion-induced changes in cartilage's properties reveal a complex relationship between the molecular weight and concentration of the HA in the interstitial fluid, and the structure and properties of the collagen fibril pore network, and provide new insights into how changes in either could influence the onset and progression of osteoarthritis.
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| 30. |
- Hamdi, Yosr, et al.
(författare)
-
Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression : identification of a modifier of breast cancer risk at locus 11q22.3
- 2017
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Ingår i: Breast Cancer Research and Treatment. - : Springer Science and Business Media LLC. - 0167-6806 .- 1573-7217. ; 161:1, s. 117-134
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Cis-acting regulatory SNPs resulting in differential allelic expression (DAE) may, in part, explain the underlying phenotypic variation associated with many complex diseases. To investigate whether common variants associated with DAE were involved in breast cancer susceptibility among BRCA1 and BRCA2 mutation carriers, a list of 175 genes was developed based of their involvement in cancer-related pathways. Methods: Using data from a genome-wide map of SNPs associated with allelic expression, we assessed the association of ~320 SNPs located in the vicinity of these genes with breast and ovarian cancer risks in 15,252 BRCA1 and 8211 BRCA2 mutation carriers ascertained from 54 studies participating in the Consortium of Investigators of Modifiers of BRCA1/2. Results: We identified a region on 11q22.3 that is significantly associated with breast cancer risk in BRCA1 mutation carriers (most significant SNP rs228595 p = 7 × 10−6). This association was absent in BRCA2 carriers (p = 0.57). The 11q22.3 region notably encompasses genes such as ACAT1, NPAT, and ATM. Expression quantitative trait loci associations were observed in both normal breast and tumors across this region, namely for ACAT1, ATM, and other genes. In silico analysis revealed some overlap between top risk-associated SNPs and relevant biological features in mammary cell data, which suggests potential functional significance. Conclusion: We identified 11q22.3 as a new modifier locus in BRCA1 carriers. Replication in larger studies using estrogen receptor (ER)-negative or triple-negative (i.e., ER-, progesterone receptor-, and HER2-negative) cases could therefore be helpful to confirm the association of this locus with breast cancer risk.
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| 31. |
- Jacobs, Kevin B, et al.
(författare)
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Detectable clonal mosaicism and its relationship to aging and cancer.
- 2012
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Ingår i: Nature Genetics. - New York : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 44:6, s. 651-658
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Tidskriftsartikel (refereegranskat)abstract
- In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
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| 32. |
- Leisawitz, David, et al.
(författare)
-
Origins Space Telescope: Baseline mission concept
- 2021
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Ingår i: Journal of Astronomical Telescopes, Instruments, and Systems. - 2329-4221 .- 2329-4124. ; 7:1
-
Tidskriftsartikel (refereegranskat)abstract
- The Origins Space Telescope will trace the history of our origins from the time dust and heavy elements permanently altered the cosmic landscape to present-day life. How did galaxies evolve from the earliest galactic systems to those found in the Universe today? How do habitable planets form? How common are life-bearing worlds? To answer these alluring questions, Origins will operate at mid-and far-infrared (IR) wavelengths and offer powerful spectroscopic instruments and sensitivity three orders of magnitude better than that of the Herschel Space Observatory, the largest telescope flown in space to date. We describe the baseline concept for Origins recommended to the 2020 US Decadal Survey in Astronomy and Astrophysics. The baseline design includes a 5.9-m diameter telescope cryocooled to 4.5 K and equipped with three scientific instruments. A mid-infrared instrument (Mid-Infrared Spectrometer and Camera Transit spectrometer) will measure the spectra of transiting exoplanets in the 2.8 to 20 μm wavelength range and offer unprecedented spectrophotometric precision, enabling definitive exoplanet biosignature detections. The far-IR imager polarimeter will be able to survey thousands of square degrees with broadband imaging at 50 and 250 μm. The Origins Survey Spectrometer will cover wavelengths from 25 to 588 μm, making wide-area and deep spectroscopic surveys with spectral resolving power R ∼ 300, and pointed observations at R ∼ 40,000 and 300,000 with selectable instrument modes. Origins was designed to minimize complexity. The architecture is similar to that of the Spitzer Space Telescope and requires very few deployments after launch, while the cryothermal system design leverages James Webb Space Telescope technology and experience. A combination of current-state-of-the-art cryocoolers and next-generation detector technology will enable Origins' natural background-limited sensitivity.
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| 33. |
- Lindauer, Matthew, et al.
(författare)
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Comparing the effect of rational and emotional appeals on donation behavior
- 2020
-
Ingår i: Judgment and Decision Making. - Tallahassee, FL United States : Society for Judgment and Decision Making. - 1930-2975. ; 15:3, s. 413-420
-
Tidskriftsartikel (refereegranskat)abstract
- We present evidence from a pre-registered experiment indicating that a philosophical argument - a type of rational appeal - can persuade people to make charitable donations. The rational appeal we used follows Singers "shallow pond" argument (1972), while incorporating an evolutionary debunking argument (Paxton, Ungar and Greene, 2012) against favoring nearby victims over distant ones. The effectiveness of this rational appeal did not differ significantly from that of a well-tested emotional appeal involving an image of a single child in need (Small, Loewenstein and Slovic, 2007). This is a surprising result, given evidence that emotions are the primary drivers of moral action, a view that has been very influential in the work of development organizations. We found no support for our hypothesis that combining our rational and emotional appeals would have a stronger effect than either appeal in isolation. However, our finding that both kinds of appeal can increase charitable donations is cause for optimism, especially concerning the potential efficacy of well-designed rational appeals. We consider the significance of these findings for moral psychology, ethics, and the work of organizations aiming to alleviate severe poverty.
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| 34. |
- Madsen, Lynette D, et al.
(författare)
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Texture of Al thin films deposited by magnetron sputtering onto epitaxial W(001)
- 2000
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 87:1, s. 168-171
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Tidskriftsartikel (refereegranskat)abstract
- Highly textured epitaxial metallizations will be required for the next generation of devices with the main driving force being a reduction in electromigration. Herein a model system of 190 nm of Al on a 140 nm layer of W grown on MgO less than 00l greater than substrates was studied. The W layer was less than 00l greater than oriented and rotated 45 degrees with respect to the MgO substrate to minimize the misfit; the remaining strain was accommodated by dislocations, evident in transmission electron microscopy images. From high-resolution x-ray diffraction (XRD) measurements, the out-of-plane lattice parameter was determined to be 3.175 Angstrom, and the in-plane parameter was 3.153 Angstrom, i.e., the W film sustained a strain resulting in a tetragonal distortion of the lattice. XRD pole figures showed that the Al had four fold symmetry and two dominant orientations, less than 016 greater than and less than 3 9 11 greater than, which were twinned with multiple placements on the epitaxial W layer. The driving force for the tilted less than 001 greater than and less than 011 greater than orientations of Al on W is due to strain minimization through lattice matching. These results show that less than 00l greater than Al deposited at ambient conditions onto W is difficult to achieve and implies that electromigration difficulties are inherent.
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| 35. |
- Nedfors, Nils, et al.
(författare)
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The influence of pressure and magnetic field on the deposition of epitaxial TiBx thin films from DC magnetron sputtering
- 2020
-
Ingår i: Vacuum. - : Elsevier BV. - 0042-207X .- 1879-2715. ; 177
-
Tidskriftsartikel (refereegranskat)abstract
- Magnetron sputter deposition of TiBx thin films from a TiB2 target typically results in highly overstoichiometric films due to differences in sputtered-atom ejection angles and gas-phase scattering during transport to the substrate. This study investigates the effects of the magnetron magnetic field strength at the substrate position and the Ar sputtering pressure on the resulting film composition and crystalline quality. It is shown that the B/Ti atomic ratio can be reduced from 2.7 to 2.1 by increasing the Ar pressure from 5 mTorr to 20 mTorr, a trend consistent with previous work. Despite the use of a relatively high Ar pressure, a change to a stronger outer magnetic pole leads to, dense TiB2.1 films of high crystal quality, as shown by X-ray diffraction, scanning transmission electron microscopy, and specific resistivity of 32 mu Omega cm. For epitaxial films deposited at 900 degrees C on Al2O3(001), a TiB2[110]//Al2O3[100] orientational relationship were obtained.
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| 36. |
- Osorio, Ana, et al.
(författare)
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DNA Glycosylases Involved in Base Excision Repair May Be Associated with Cancer Risk in BRCA1 and BRCA2 Mutation Carriers.
- 2014
-
Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 10:4
-
Tidskriftsartikel (refereegranskat)abstract
- Single Nucleotide Polymorphisms (SNPs) in genes involved in the DNA Base Excision Repair (BER) pathway could be associated with cancer risk in carriers of mutations in the high-penetrance susceptibility genes BRCA1 and BRCA2, given the relation of synthetic lethality that exists between one of the components of the BER pathway, PARP1 (poly ADP ribose polymerase), and both BRCA1 and BRCA2. In the present study, we have performed a comprehensive analysis of 18 genes involved in BER using a tagging SNP approach in a large series of BRCA1 and BRCA2 mutation carriers. 144 SNPs were analyzed in a two stage study involving 23,463 carriers from the CIMBA consortium (the Consortium of Investigators of Modifiers of BRCA1 and BRCA2). Eleven SNPs showed evidence of association with breast and/or ovarian cancer at p<0.05 in the combined analysis. Four of the five genes for which strongest evidence of association was observed were DNA glycosylases. The strongest evidence was for rs1466785 in the NEIL2 (endonuclease VIII-like 2) gene (HR: 1.09, 95% CI (1.03-1.16), p = 2.7×10-3) for association with breast cancer risk in BRCA2 mutation carriers, and rs2304277 in the OGG1 (8-guanine DNA glycosylase) gene, with ovarian cancer risk in BRCA1 mutation carriers (HR: 1.12 95%CI: 1.03-1.21, p = 4.8×10-3). DNA glycosylases involved in the first steps of the BER pathway may be associated with cancer risk in BRCA1/2 mutation carriers and should be more comprehensively studied.
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| 37. |
- Rebbeck, Timothy R., et al.
(författare)
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Inheritance of deleterious mutations at both BRCA1 and BRCA2 in an international sample of 32,295 women
- 2016
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Ingår i: Breast Cancer Research. - : Springer Science and Business Media LLC. - 1465-5411 .- 1465-542X. ; 18:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Most BRCA1 or BRCA2 mutation carriers have inherited a single (heterozygous) mutation. Transheterozygotes (TH) who have inherited deleterious mutations in both BRCA1 and BRCA2 are rare, and the consequences of transheterozygosity are poorly understood. Methods: From 32,295 female BRCA1/2 mutation carriers, we identified 93 TH (0.3 %). "Cases" were defined as TH, and "controls" were single mutations at BRCA1 (SH1) or BRCA2 (SH2). Matched SH1 "controls" carried a BRCA1 mutation found in the TH "case". Matched SH2 "controls" carried a BRCA2 mutation found in the TH "case". After matching the TH carriers with SH1 or SH2, 91 TH were matched to 9316 SH1, and 89 TH were matched to 3370 SH2. Results: The majority of TH (45.2 %) involved the three common Jewish mutations. TH were more likely than SH1 and SH2 women to have been ever diagnosed with breast cancer (BC; p = 0.002). TH were more likely to be diagnosed with ovarian cancer (OC) than SH2 (p = 0.017), but not SH1. Age at BC diagnosis was the same in TH vs. SH1 (p = 0.231), but was on average 4.5 years younger in TH than in SH2 (p < 0.001). BC in TH was more likely to be estrogen receptor (ER) positive (p = 0.010) or progesterone receptor (PR) positive (p = 0.013) than in SH1, but less likely to be ER positive (p < 0.001) or PR positive (p = 0.012) than SH2. Among 15 tumors from TH patients, there was no clear pattern of loss of heterozygosity (LOH) for BRCA1 or BRCA2 in either BC or OC. Conclusions: Our observations suggest that clinical TH phenotypes resemble SH1. However, TH breast tumor marker characteristics are phenotypically intermediate to SH1 and SH2.
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| 38. |
- Sangiovanni, Davide, et al.
(författare)
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Ab-initio and classical molecular dynamics simulations of N2 desorption from TiN(001) surfaces
- 2014
-
Ingår i: Surface Science. - : Elsevier. - 0039-6028 .- 1879-2758. ; 624, s. 25-31
-
Tidskriftsartikel (refereegranskat)abstract
- Ab initio molecular dynamics simulations based on density functional theory show that N adatoms are chemisorbed in threefold sites close to a N surface atom and between the two diagonally opposed neighboring Ti surface atoms on TiN(001). The most probable N adatom reaction pathway, even in the presence of nearby N adatoms, is for the N adatom and N surface atom pair to first undergo several exchange reactions and then desorb as a N2 molecule, resulting in a surface anion vacancy, with an activation barrier Edes of 1.37 eV and an attempt frequency Ades = 3.4 × 1013 s− 1. Edes is essentially equal to the N adatom surface diffusion barrier, Es = 1.39 eV, while As is only three to four times larger than Ades, indicating that isolated N adatoms migrate for only short distances prior to N2 desorption. The probability of N2 desorption via recombination of N adatoms on TiN(001) is much lower due to repulsive adatom/adatom interactions at separations less than ~ 3 Å which rapidly increase to ~ 2 eV at a separation of 1.5 Å. We obtain good qualitative and quantitative agreement with the above results using the modified embedded atom method potential to perform classical molecular dynamics simulations.
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| 39. |
- Sangiovanni, Davide, et al.
(författare)
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Dynamics of Ti, N, and TiNx (x=1-3) admolecule transport on TiN(001) surfaces
- 2012
-
Ingår i: Physical Review B. Condensed Matter and Materials Physics. - : American Physical Society. - 1098-0121 .- 1550-235X. ; 86:15, s. 155443-
-
Tidskriftsartikel (refereegranskat)abstract
- We use classical molecular dynamics and the modified embedded atom method formalism to investigate the dynamics of atomic-scale transport on a low-index model compound surface, TiN(001). Our simulations, totaling 0.25 mu s for each case study, follow the pathways and migration kinetics of Ti and N adatoms, as well as TiNx complexes with x = 1-3, which are known to contribute to the growth of TiN thin films by reactive deposition from Ti, N-2, and N precursors. The simulations are carried out at 1000 K, within the optimal range for TiN(001) epitaxial growth. We find Ti adatoms to be the highest-mobility species on TiN(001), with the primary migration path involving jumps of one nearest-neighbor distance d(NN) between adjacent fourfold hollow sites along in-plane andlt; 100 andgt; channels. Long jumps, 2d(NN), are also observed, but at much lower frequency. N adatoms, which exhibit significantly lower migration rates than Ti, diffuse along in-plane andlt; 110 andgt; directions and, when they intersect other N atoms, associatively form N-2 molecules, which desorb at kinetic rates. As expected, TiN and TiN3 complexes migrate at even lower rates with complex diffusion pathways involving rotations, translations, and rototranslations. TiN2 trimers, however, are shown to have surprisingly high diffusion rates, above that of N adatoms and almost half that of Ti adatoms. TiN3 motion is dominated by in-place rotation with negligible diffusion.
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| 40. |
- Sangiovanni, Davide, et al.
(författare)
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Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands
- 2018
-
Ingår i: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 97:3
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Tidskriftsartikel (refereegranskat)abstract
- We carried out density-functional ab initio molecular dynamics (AIMD) simulations of Ti adatom (Ti-ad ) migration on, and descent from, square TiN(100) epitaxial islands on TiN(001) at temperatures (T) ranging from 1200 to 2400 K. Adatom-descent energy barriers determined via ab initio nudged-elastic-band calculations at 0 Kelvin suggest that Ti interlayer transport on TiN(001) occurs essentially exclusively via direct hopping onto a lower layer. However, AIMD simulations reveal comparable rates for Ti-ad descent via direct hopping vs push-out/exchange with a Ti island-edge atom for T amp;gt;= 1500 K. We demonstrate that this effect is due to surface vibrations, which yield considerably lower activation energies at finite temperatures by significantly modifying the adatom push-out/exchange reaction pathway.
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| 41. |
- Sangiovanni, Davide, et al.
(författare)
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Ti adatom diffusion on TiN(001) : Ab initio and classical molecular dynamics simulations
- 2014
-
Ingår i: Surface Science. - : Elsevier. - 0039-6028 .- 1879-2758. ; 627, s. 34-41
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Tidskriftsartikel (refereegranskat)abstract
- Ab initio and classical molecular dynamics (AIMD and CMD) simulations reveal that Ti adatoms on TiN(001) surfaces migrate between neighboring fourfold hollow sites primarily along in-plane less than100greater than channels. less than100greater than and less than110greater than single jumps, as well as less than100greater than double jump rates, obtained directly from MD runs as a function of temperature, are used to determine diffusion activation energies Ea, and attempt frequencies A, for the three preferred Ti adatom migration pathways on TiN(001). From transition rates Aexp[-Ea / (k(B)T)], we determine adatom surface distribution probabilities as a function of time, which are used to calculate adatom diffusion coefficients D(T). AIMD and CMD predictions are consistent and complementary. Using CMD, we investigate the effect on the adatom jump rate of varying the phonon wavelength degrees of freedom by progressively increasing the supercell size. We find that long-wavelength phonons significantly contribute to increasing adatom mobilities at temperatures less than= 600 K, but not at higher temperatures. Finally, by directly tracking the Ti adatom mean-square displacement during CMD runs, we find that Ti adatom jumps are highly correlated on TiN(001), an effect that yields lower D-s values (D-s(corr)) than those estimated from uncorrelated transition probabilities. The temperature-dependent diffusion coefficient is D-s(corr) (T) = (4.5 x 10(-4) Cm-2 s(-1)) exp[-0.55 eV / (k(B)T)].
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| 42. |
- Villamayor, Michelle M, et al.
(författare)
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Low temperature (T-s/T-m < 0.1) epitaxial growth of HfN/MgO(001) via reactive HiPIMS with metal-ion synchronized substrate bias
- 2018
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Ingår i: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : A V S AMER INST PHYSICS. - 0734-2101 .- 1520-8559. ; 36:6
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Tidskriftsartikel (refereegranskat)abstract
- Low-temperature epitaxial growth of refractory transition-metal nitride thin films by means of physical vapor deposition has been a recurring theme in advanced thin-film technology for several years. In the present study, 150-nm-thick epitaxial HfN layers are grown on MgO(001) by reactive high-power impulse magnetron sputtering (HiPIMS) with no external substrate heating. Maximum film-growth temperatures T-s due to plasma heating range from 70 to 150 degrees C, corresponding to T-s/T-m = 0.10-0.12 (in which T-m is the HfN melting point in K). During HiPIMS, gas and sputtered metal-ion fluxes incident at the growing film surface are separated in time due to strong gas rarefaction and the transition to a metal-ion-dominated plasma. In the present experiments, a negative bias of 100 V is applied to the substrate, either continuously during the entire deposition or synchronized with the metal-rich portion of the ion flux. Two different sputtering-gas mixtures, Ar/N-2 and Kr/N-2, are employed in order to probe effects associated with the noble-gas mass and ionization potential. The combination of x-ray diffraction, high-resolution reciprocal-lattice maps, and high-resolution cross-sectional transmission electron microscopy analyses establishes that all HfN films have a cube-on-cube orientational relationship with the substrate, i.e., [001](HfN)parallel to[001](MgO) and (100)(HfN)parallel to(100)(MgO). Layers grown with a continuous substrate bias, in either Ar/N-2 or Kr/N-2, exhibit a relatively high mosaicity and a high concentration of trapped inert gas. In distinct contrast, layers grown in Kr/N-2 with the substrate bias synchronized to the metal-ion-rich portion of HiPIMS pulses have much lower mosaicity, no measurable inert-gas incorporation, and a hardness of 25.7 GPa, in good agreement with the results for epitaxial HfN(001) layers grown at T-s = 650 degrees C (T-s/T-m = 0.26). The room-temperature film resistivity is 70 mu Omega cm, which is 3.2-10 times lower than reported values for polycrystalline-HfN layers grown at T-s = 400 degrees C. (c) 2018 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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| 43. |
- Wang, Zhaoming, et al.
(författare)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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