| 1. |
- Alessandro, B., et al.
(author)
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Vector boson scattering : Recent experimental and theory developments
- 2018
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In: Reviews in Physics. - : Elsevier BV. - 2405-4283. ; 3, s. 44-63
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Journal article (peer-reviewed)abstract
- This document summarises the talks and discussions happened during the VBSCan Split17 workshop, the first general meeting of the VBSCan COST Action network. This collaboration is aiming at a consistent and coordinated study of vector-boson scattering from the phenomenological and experimental point of view, for the best exploitation of the data that will be delivered by existing and future particle colliders.
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| 2. |
- Chen, Zhishan, et al.
(author)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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| 3. |
- Barack, Leor, et al.
(author)
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Black holes, gravitational waves and fundamental physics : a roadmap
- 2019
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In: Classical and quantum gravity. - : IOP Publishing. - 0264-9381 .- 1361-6382. ; 36:14
-
Research review (peer-reviewed)abstract
- The grand challenges of contemporary fundamental physics dark matter, dark energy, vacuum energy, inflation and early universe cosmology, singularities and the hierarchy problem all involve gravity as a key component. And of all gravitational phenomena, black holes stand out in their elegant simplicity, while harbouring some of the most remarkable predictions of General Relativity: event horizons, singularities and ergoregions. The hitherto invisible landscape of the gravitational Universe is being unveiled before our eyes: the historical direct detection of gravitational waves by the LIGO-Virgo collaboration marks the dawn of a new era of scientific exploration. Gravitational-wave astronomy will allow us to test models of black hole formation, growth and evolution, as well as models of gravitational-wave generation and propagation. It will provide evidence for event horizons and ergoregions, test the theory of General Relativity itself, and may reveal the existence of new fundamental fields. The synthesis of these results has the potential to radically reshape our understanding of the cosmos and of the laws of Nature. The purpose of this work is to present a concise, yet comprehensive overview of the state of the art in the relevant fields of research, summarize important open problems, and lay out a roadmap for future progress. This write-up is an initiative taken within the framework of the European Action on 'Black holes, Gravitational waves and Fundamental Physics'.
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| 4. |
- Murphy, Neil, et al.
(author)
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Body mass index and molecular subtypes of colorectal cancer
- 2023
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In: Journal of the National Cancer Institute. - : Oxford University Press. - 0027-8874 .- 1460-2105. ; 115:2, s. 165-173
-
Journal article (peer-reviewed)abstract
- Background: Obesity is an established risk factor for colorectal cancer (CRC), but the evidence for the association is inconsistent across molecular subtypes of the disease.Methods: We pooled data on body mass index (BMI), tumor microsatellite instability status, CpG island methylator phenotype status, BRAF and KRAS mutations, and Jass classification types for 11 872 CRC cases and 11 013 controls from 11 observational studies. We used multinomial logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) adjusted for covariables.Results: Higher BMI was associated with increased CRC risk (OR per 5 kg/m(2) = 1.18, 95% CI = 1.15 to 1.22). The positive association was stronger for men than women but similar across tumor subtypes defined by individual molecular markers. In analyses by Jass type, higher BMI was associated with elevated CRC risk for types 1-4 cases but not for type 5 CRC cases (considered familial-like/Lynch syndrome microsatellite instability-H, CpG island methylator phenotype-low or negative, BRAF-wild type, KRAS-wild type, OR = 1.04, 95% CI = 0.90 to 1.20). This pattern of associations for BMI and Jass types was consistent by sex and design of contributing studies (cohort or case-control).Conclusions: In contrast to previous reports with fewer study participants, we found limited evidence of heterogeneity for the association between BMI and CRC risk according to molecular subtype, suggesting that obesity influences nearly all major pathways involved in colorectal carcinogenesis. The null association observed for the Jass type 5 suggests that BMI is not a risk factor for the development of CRC for individuals with Lynch syndrome.
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| 5. |
- Backes, Claudia, et al.
(author)
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Production and processing of graphene and related materials
- 2020
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In: 2D Materials. - : IOP Publishing. - 2053-1583. ; 7:2
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Journal article (peer-reviewed)abstract
- We present an overview of the main techniques for production and processing of graphene and related materials (GRMs), as well as the key characterization procedures. We adopt a 'hands-on' approach, providing practical details and procedures as derived from literature as well as from the authors' experience, in order to enable the reader to reproduce the results. Section I is devoted to 'bottom up' approaches, whereby individual constituents are pieced together into more complex structures. We consider graphene nanoribbons (GNRs) produced either by solution processing or by on-surface synthesis in ultra high vacuum (UHV), as well carbon nanomembranes (CNM). Production of a variety of GNRs with tailored band gaps and edge shapes is now possible. CNMs can be tuned in terms of porosity, crystallinity and electronic behaviour. Section II covers 'top down' techniques. These rely on breaking down of a layered precursor, in the graphene case usually natural crystals like graphite or artificially synthesized materials, such as highly oriented pyrolythic graphite, monolayers or few layers (FL) flakes. The main focus of this section is on various exfoliation techniques in a liquid media, either intercalation or liquid phase exfoliation (LPE). The choice of precursor, exfoliation method, medium as well as the control of parameters such as time or temperature are crucial. A definite choice of parameters and conditions yields a particular material with specific properties that makes it more suitable for a targeted application. We cover protocols for the graphitic precursors to graphene oxide (GO). This is an important material for a range of applications in biomedicine, energy storage, nanocomposites, etc. Hummers' and modified Hummers' methods are used to make GO that subsequently can be reduced to obtain reduced graphene oxide (RGO) with a variety of strategies. GO flakes are also employed to prepare three-dimensional (3d) low density structures, such as sponges, foams, hydro- or aerogels. The assembly of flakes into 3d structures can provide improved mechanical properties. Aerogels with a highly open structure, with interconnected hierarchical pores, can enhance the accessibility to the whole surface area, as relevant for a number of applications, such as energy storage. The main recipes to yield graphite intercalation compounds (GICs) are also discussed. GICs are suitable precursors for covalent functionalization of graphene, but can also be used for the synthesis of uncharged graphene in solution. Degradation of the molecules intercalated in GICs can be triggered by high temperature treatment or microwave irradiation, creating a gas pressure surge in graphite and exfoliation. Electrochemical exfoliation by applying a voltage in an electrolyte to a graphite electrode can be tuned by varying precursors, electrolytes and potential. Graphite electrodes can be either negatively or positively intercalated to obtain GICs that are subsequently exfoliated. We also discuss the materials that can be amenable to exfoliation, by employing a theoretical data-mining approach. The exfoliation of LMs usually results in a heterogeneous dispersion of flakes with different lateral size and thickness. This is a critical bottleneck for applications, and hinders the full exploitation of GRMs produced by solution processing. The establishment of procedures to control the morphological properties of exfoliated GRMs, which also need to be industrially scalable, is one of the key needs. Section III deals with the processing of flakes. (Ultra)centrifugation techniques have thus far been the most investigated to sort GRMs following ultrasonication, shear mixing, ball milling, microfluidization, and wet-jet milling. It allows sorting by size and thickness. Inks formulated from GRM dispersions can be printed using a number of processes, from inkjet to screen printing. Each technique has specific rheological requirements, as well as geometrical constraints. The solvent choice is critical, not only for the GRM stability, but also in terms of optimizing printing on different substrates, such as glass, Si, plastic, paper, etc, all with different surface energies. Chemical modifications of such substrates is also a key step. Sections IV-VII are devoted to the growth of GRMs on various substrates and their processing after growth to place them on the surface of choice for specific applications. The substrate for graphene growth is a key determinant of the nature and quality of the resultant film. The lattice mismatch between graphene and substrate influences the resulting crystallinity. Growth on insulators, such as SiO2, typically results in films with small crystallites, whereas growth on the close-packed surfaces of metals yields highly crystalline films. Section IV outlines the growth of graphene on SiC substrates. This satisfies the requirements for electronic applications, with well-defined graphene-substrate interface, low trapped impurities and no need for transfer. It also allows graphene structures and devices to be measured directly on the growth substrate. The flatness of the substrate results in graphene with minimal strain and ripples on large areas, allowing spectroscopies and surface science to be performed. We also discuss the surface engineering by intercalation of the resulting graphene, its integration with Si-wafers and the production of nanostructures with the desired shape, with no need for patterning. Section V deals with chemical vapour deposition (CVD) onto various transition metals and on insulators. Growth on Ni results in graphitized polycrystalline films. While the thickness of these films can be optimized by controlling the deposition parameters, such as the type of hydrocarbon precursor and temperature, it is difficult to attain single layer graphene (SLG) across large areas, owing to the simultaneous nucleation/growth and solution/precipitation mechanisms. The differing characteristics of polycrystalline Ni films facilitate the growth of graphitic layers at different rates, resulting in regions with differing numbers of graphitic layers. High-quality films can be grown on Cu. Cu is available in a variety of shapes and forms, such as foils, bulks, foams, thin films on other materials and powders, making it attractive for industrial production of large area graphene films. The push to use CVD graphene in applications has also triggered a research line for the direct growth on insulators. The quality of the resulting films is lower than possible to date on metals, but enough, in terms of transmittance and resistivity, for many applications as described in section V. Transfer technologies are the focus of section VI. CVD synthesis of graphene on metals and bottom up molecular approaches require SLG to be transferred to the final target substrates. To have technological impact, the advances in production of high-quality large-area CVD graphene must be commensurate with those on transfer and placement on the final substrates. This is a prerequisite for most applications, such as touch panels, anticorrosion coatings, transparent electrodes and gas sensors etc. New strategies have improved the transferred graphene quality, making CVD graphene a feasible option for CMOS foundries. Methods based on complete etching of the metal substrate in suitable etchants, typically iron chloride, ammonium persulfate, or hydrogen chloride although reliable, are time- and resource-consuming, with damage to graphene and production of metal and etchant residues. Electrochemical delamination in a low-concentration aqueous solution is an alternative. In this case metallic substrates can be reused. Dry transfer is less detrimental for the SLG quality, enabling a deterministic transfer. There is a large range of layered materials (LMs) beyond graphite. Only few of them have been already exfoliated and fully characterized. Section VII deals with the growth of some of these materials. Amongst them, h-BN, transition metal tri- and di-chalcogenides are of paramount importance. The growth of h-BN is at present considered essential for the development of graphene in (opto) electronic applications, as h-BN is ideal as capping layer or substrate. The interesting optical and electronic properties of TMDs also require the development of scalable methods for their production. Large scale growth using chemical/physical vapour deposition or thermal assisted conversion has been thus far limited to a small set, such as h-BN or some TMDs. Heterostructures could also be directly grown. Section VIII discusses advances in GRM functionalization. A broad range of organic molecules can be anchored to the sp(2) basal plane by reductive functionalization. Negatively charged graphene can be prepared in liquid phase (e.g. via intercalation chemistry or electrochemically) and can react with electrophiles. This can be achieved both in dispersion or on substrate. The functional groups of GO can be further derivatized. Graphene can also be noncovalently functionalized, in particular with polycyclic aromatic hydrocarbons that assemble on the sp(2) carbon network by pi-pi stacking. In the liquid phase, this can enhance the colloidal stability of SLG/FLG. Approaches to achieve noncovalent on-substrate functionalization are also discussed, which can chemically dope graphene. Research efforts to derivatize CNMs are also summarized, as well as novel routes to selectively address defect sites. In dispersion, edges are the most dominant defects and can be covalently modified. This enhances colloidal stability without modifying the graphene basal plane. Basal plane point defects can also be modified, passivated and healed in ultra-high vacuum. The decoration of graphene with metal nanoparticles (NPs) has also received considerable attention, as it allows to exploit synergistic effects between NPs and graphene. Decoration can be either achieved chemically or in the gas phase. All LMs,
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| 6. |
- Bauer, Michael, et al.
(author)
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Association between solar insolation and a history of suicide attempts in bipolar I disorder.
- 2019
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In: Journal of psychiatric research. - : Elsevier BV. - 1879-1379 .- 0022-3956. ; 113, s. 1-9
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Journal article (peer-reviewed)abstract
- In many international studies, rates of completed suicide and suicide attempts have a seasonal pattern that peaks in spring or summer. This exploratory study investigated the association between solar insolation and a history of suicide attempt in patients with bipolar I disorder. Solar insolation is the amount of electromagnetic energy from the Sun striking a surface area on Earth. Data were collected previously from 5536 patients with bipolar I disorder at 50 collection sites in 32 countries at a wide range of latitudes in both hemispheres. Suicide related data were available for 3365 patients from 310 onset locations in 51 countries. 1047 (31.1%) had a history of suicide attempt. There was a significant inverse association between a history of suicide attempt and the ratio of mean winter solar insolation/mean summer solar insolation. This ratio is smallest near the poles where the winter insolation is very small compared to the summer insolation. This ratio is largest near the equator where there is relatively little variation in the insolation over the year. Other variables in the model that were positively associated with suicide attempt were being female, a history of alcohol or substance abuse, and being in a younger birth cohort. Living in a country with a state-sponsored religion decreased the association. (All estimated coefficients p<0.01). In summary, living in locations with large changes in solar insolation between winter and summer may be associated with increased suicide attempts in patients with bipolar disorder. Further investigation of the impacts of solar insolation on the course of bipolar disorder is needed.
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| 7. |
- Castro-Espin, Carlota, et al.
(author)
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Association of Mediterranean diet with survival after breast cancer diagnosis in women from nine European countries : results from the EPIC cohort study
- 2023
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In: BMC Medicine. - : BioMed Central (BMC). - 1741-7015. ; 21:1
-
Journal article (peer-reviewed)abstract
- Background: The Mediterranean diet has been associated with lower risk of breast cancer (BC) but evidence from prospective studies on the role of Mediterranean diet on BC survival remains sparse and conflicting. We aimed to investigate whether adherence to Mediterranean diet prior to diagnosis is associated with overall and BC-specific mortality.Methods: A total of 13,270 incident breast cancer cases were identified from an initial sample of 318,686 women in 9 countries from the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Adherence to Mediterranean diet was estimated through the adapted relative Mediterranean diet (arMED), a 16-point score that includes 8 key components of the Mediterranean diet and excludes alcohol. The degree of adherence to arMED was classified as low (score 0–5), medium (score 6–8), and high (score 9–16). Multivariable Cox proportional hazards models were used to analyze the association between the arMED score and overall mortality, and Fine-Gray competing risks models were applied for BC-specific mortality.Results: After a mean follow-up of 8.6 years from diagnosis, 2340 women died, including 1475 from breast cancer. Among all BC survivors, low compared to medium adherence to arMED score was associated with a 13% higher risk of all-cause mortality (HR 1.13, 95%CI 1.01–1.26). High compared to medium adherence to arMED showed a non-statistically significant association (HR 0.94; 95% CI 0.84–1.05). With no statistically significant departures from linearity, on a continuous scale, a 3-unit increase in the arMED score was associated with an 8% reduced risk of overall mortality (HR3-unit 0.92, 95% CI: 0.87–0.97). This result sustained when restricted to postmenopausal women and was stronger among metastatic BC cases (HR3-unit 0.81, 95% CI: 0.72–0.91).Conclusions: Consuming a Mediterranean diet before BC diagnosis may improve long-term prognosis, particularly after menopause and in cases of metastatic breast cancer. Well-designed dietary interventions are needed to confirm these findings and define specific dietary recommendations.
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| 8. |
- Huybrechts, Inge, et al.
(author)
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Food biodiversity and gastrointestinal cancer risk in nine European countries : analysis within a prospective cohort study
- 2024
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In: European Journal of Cancer. - : Elsevier. - 0959-8049 .- 1879-0852. ; 210
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Journal article (peer-reviewed)abstract
- Background: Food biodiversity in human diets has potential co-benefits for both public health and sustainable food systems. However, current evidence on the potential relationship between food biodiversity and cancer risk, and particularly gastrointestinal cancers typically related to diet, remains limited. This study evaluated how dietary species richness (DSR) was associated with gastrointestinal cancer risk in a pan-European population.Methods: Associations between DSR and subsequent gastrointestinal cancer risk were examined among 450,111 adults enrolled in the European Prospective Investigation into Cancer and Nutrition cohort (EPIC, initiated in 1992), free of cancer at baseline. Usual dietary intakes were assessed at recruitment with country-specific dietary questionnaires. DSR of an individual's yearly diet was calculated based on the absolute number of unique biological species in each food and drink item. Associations between DSR and cancer risk were assessed by multivariable Cox proportional hazards regression models.Findings: During a median follow-up time of 14.1 years (SD=3.9), 10,705 participants were diagnosed with gastrointestinal cancer. Hazard ratios (HRs) and 95 % confidence intervals (CIs) comparing overall gastrointestinal cancer risk in the highest versus lowest quintiles of DSR indicated inverse associations in multivariable-adjusted models [HR (95 % CI): 0.77 (0.69–0.87); P-value < 0·0001] (Table 2). Specifically, inverse associations were observed between DSR and oesophageal squamous cell carcinoma, proximal colon, colorectal, and liver cancer risk (p-trend<0.05 for all cancer types).Interpretation: Greater food biodiversity in the diet may lower the risk of certain gastrointestinal cancers. Further research is needed to replicate these novel findings and to understand potential mechanisms.
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| 9. |
- Mayén, Ana-Lucia, et al.
(author)
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Hepatic steatosis, metabolic dysfunction and risk of mortality : findings from a multinational prospective cohort study
- 2024
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In: BMC Medicine. - : BioMed Central (BMC). - 1741-7015. ; 22:1
-
Journal article (peer-reviewed)abstract
- BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) and metabolic syndrome (MetS) are implicated in the aetiology of non-communicable diseases. Our study aimed to evaluate associations between NAFLD and MetS with overall and cause-specific mortality.METHODS: We used dietary, lifestyle, anthropometric and metabolic biomarker data from a random subsample of 15,784 EPIC cohort participants. NAFLD was assessed using the fatty liver index (FLI) and MetS using the revised definition. Indices for metabolic dysfunction-associated fatty liver disease (MAFLD) were calculated. The individual associations of these indices with overall and cause-specific mortality were assessed using multivariable Cox proportional hazards models to estimate hazard ratios (HRs) and 95% confidence intervals (95%CIs). As a subobjective, risk associations with adaptations of new classifications of metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic and alcohol-related liver disease (MetALD) were also assessed.RESULTS: Among the 15,784 sub-cohort participants, a total of 1997 deaths occurred (835 due to cancer, 520 to CVD, 642 to other causes) over a median 15.6 (IQR, 12.3-17.1) years of follow-up. Compared to an FLI < 30, FLI ≥ 60 was associated with increased risks of overall mortality (HR = 1.44, 95%CI = 1.27-1.63), and deaths from cancer (HR = 1.32, 95%CI = 1.09-1.60), CVD (HR = 2.06, 95% CI = 1.61-2.63) or other causes (HR = 1.21, 95%CI = 0.97-1.51). Mortality risk associations were also elevated for individuals with MAFLD compared to those without. Individuals with MetS were at increased risk of all mortality endpoints, except cancer-specific mortality. MASLD and MetALD were associated with higher risk of overall mortality.CONCLUSIONS: Our findings based on a prospective cohort suggest that individuals with hepatic steatosis or metabolic dysfunction have a higher overall and cause-specific mortality risk.
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| 10. |
- Sarakinos, Kostas, 1980-, et al.
(author)
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Unravelling the effect of nitrogen on the morphological evolution of thin silver films on weakly-interacting substrates
- 2024
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In: Applied Surface Science. - : Elsevier BV. - 0169-4332 .- 1873-5584. ; 649
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Journal article (peer-reviewed)abstract
- We study the effect of nitrogen on the morphological evolution of thin silver (Ag) films deposited on weakly-interacting amorphous carbon (a-C) and silicon oxide (SiOx) surfaces. Films are synthesized at a deposition rate of 0.1nm·s-1 by direct current magnetron sputtering (DCMS), high power impulse magnetron sputtering (HiPIMS), and electron-beam evaporation (EBE). We monitor growth in situ and in real time by measuring the evolution of film stress and optical properties, complemented by ex situ analyses of discontinuous-layer morphologies, film crystal structure, and film composition. We find that addition of molecular nitrogen (N2) to the plasmagenic gas (Ar) during DCMS and HiPIMS promotes a two-dimensional (2D) morphology. Concurrently, EBE-deposited films exhibit a significantly more pronounced three-dimensional morphological evolution, independently from the gas atmosphere composition. We argue that the 2D morphology in DCMS- and HiPIMS-grown films is enhanced due to incorporation of atomic nitrogen (N)—result of plasma-induced N2 dissociation—that hinders island reshaping during coalescence. This mechanism is not active during EBE due to the absence of energetic plasma electrons driving N2 dissociation. The overall results of the study show that accurate control of vapor-phase chemistry is of paramount importance when using gaseous species as agents for manipulating growth in weakly-interacting film-substrate systems.
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| 11. |
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| 12. |
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| 13. |
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| 14. |
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| 15. |
- Baliakas, Panagiotis, et al.
(author)
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Recurrent mutations refine prognosis in chronic lymphocytic leukemia
- 2015
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In: Leukemia. - : Springer Science and Business Media LLC. - 0887-6924 .- 1476-5551. ; 29, s. 329-336
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Journal article (peer-reviewed)abstract
- Through the European Research Initiative on chronic lymphocytic leukemia (CLL) (ERIC), we screened 3490 patients with CLL for mutations within the NOTCH1 (n=3334), SF3B1 (n=2322), TP53 (n=2309), MYD88 (n=1080) and BIRC3 (n=919) genes, mainly at diagnosis (75%) and before treatment (>90%). BIRC3 mutations (2.5%) were associated with unmutated IGHV genes (U-CLL), del(11q) and trisomy 12, whereas MYD88 mutations (2.2%) were exclusively found among M-CLL. NOTCH1, SF3B1 and TP53 exhibited variable frequencies and were mostly enriched within clinically aggressive cases. Interestingly, as the timespan between diagnosis and mutational screening increased, so too did the incidence of SF3B1 mutations; no such increase was observed for NOTCH1 mutations. Regarding the clinical impact, NOTCH1 mutations, SF3B1 mutations and TP53 aberrations (deletion/mutation, TP53ab) correlated with shorter time-to-first-treatment (P<0.0001) in 889 treatment-naive Binet stage A cases. In multivariate analysis (n=774), SF3B1 mutations and TP53ab along with del(11q) and U-CLL, but not NOTCH1 mutations, retained independent significance. Importantly, TP53ab and SF3B1 mutations had an adverse impact even in U-CLL. In conclusion, we support the clinical relevance of novel recurrent mutations in CLL, highlighting the adverse impact of SF3B1 and TP53 mutations, even independent of IGHV mutational status, thus underscoring the need for urgent standardization/harmonization of the detection methods.
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| 16. |
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| 17. |
- Breeur, Marie, et al.
(author)
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Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the European Prospective Investigation into Cancer and Nutrition
- 2022
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In: BMC Medicine. - : BioMed Central (BMC). - 1741-7015. ; 20:1
-
Journal article (peer-reviewed)abstract
- Background: Epidemiological studies of associations between metabolites and cancer risk have typically focused on specific cancer types separately. Here, we designed a multivariate pan-cancer analysis to identify metabolites potentially associated with multiple cancer types, while also allowing the investigation of cancer type-specific associations.Methods: We analysed targeted metabolomics data available for 5828 matched case-control pairs from cancer-specific case-control studies on breast, colorectal, endometrial, gallbladder, kidney, localized and advanced prostate cancer, and hepatocellular carcinoma nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. From pre-diagnostic blood levels of an initial set of 117 metabolites, 33 cluster representatives of strongly correlated metabolites and 17 single metabolites were derived by hierarchical clustering. The mutually adjusted associations of the resulting 50 metabolites with cancer risk were examined in penalized conditional logistic regression models adjusted for body mass index, using the data-shared lasso penalty.Results: Out of the 50 studied metabolites, (i) six were inversely associated with the risk of most cancer types: glutamine, butyrylcarnitine, lysophosphatidylcholine a C18:2, and three clusters of phosphatidylcholines (PCs); (ii) three were positively associated with most cancer types: proline, decanoylcarnitine, and one cluster of PCs; and (iii) 10 were specifically associated with particular cancer types, including histidine that was inversely associated with colorectal cancer risk and one cluster of sphingomyelins that was inversely associated with risk of hepatocellular carcinoma and positively with endometrial cancer risk.Conclusions: These results could provide novel insights for the identification of pathways for cancer development, in particular those shared across different cancer types.
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| 18. |
- Bull, Caroline J., et al.
(author)
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Adiposity, metabolites, and colorectal cancer risk : Mendelian randomization study
- 2020
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In: BMC Medicine. - : BMC. - 1741-7015. ; 18:1
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Journal article (peer-reviewed)abstract
- Background Higher adiposity increases the risk of colorectal cancer (CRC), but whether this relationship varies by anatomical sub-site or by sex is unclear. Further, the metabolic alterations mediating the effects of adiposity on CRC are not fully understood. Methods We examined sex- and site-specific associations of adiposity with CRC risk and whether adiposity-associated metabolites explain the associations of adiposity with CRC. Genetic variants from genome-wide association studies of body mass index (BMI) and waist-to-hip ratio (WHR, unadjusted for BMI; N = 806,810), and 123 metabolites from targeted nuclear magnetic resonance metabolomics (N = 24,925), were used as instruments. Sex-combined and sex-specific Mendelian randomization (MR) was conducted for BMI and WHR with CRC risk (58,221 cases and 67,694 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium, Colorectal Cancer Transdisciplinary Study, and Colon Cancer Family Registry). Sex-combined MR was conducted for BMI and WHR with metabolites, for metabolites with CRC, and for BMI and WHR with CRC adjusted for metabolite classes in multivariable models. Results In sex-specific MR analyses, higher BMI (per 4.2 kg/m(2)) was associated with 1.23 (95% confidence interval (CI) = 1.08, 1.38) times higher CRC odds among men (inverse-variance-weighted (IVW) model); among women, higher BMI (per 5.2 kg/m(2)) was associated with 1.09 (95% CI = 0.97, 1.22) times higher CRC odds. WHR (per 0.07 higher) was more strongly associated with CRC risk among women (IVW OR = 1.25, 95% CI = 1.08, 1.43) than men (IVW OR = 1.05, 95% CI = 0.81, 1.36). BMI or WHR was associated with 104/123 metabolites at false discovery rate-corrected P <= 0.05; several metabolites were associated with CRC, but not in directions that were consistent with the mediation of positive adiposity-CRC relations. In multivariable MR analyses, associations of BMI and WHR with CRC were not attenuated following adjustment for representative metabolite classes, e.g., the univariable IVW OR for BMI with CRC was 1.12 (95% CI = 1.00, 1.26), and this became 1.11 (95% CI = 0.99, 1.26) when adjusting for cholesterol in low-density lipoprotein particles. Conclusions Our results suggest that higher BMI more greatly raises CRC risk among men, whereas higher WHR more greatly raises CRC risk among women. Adiposity was associated with numerous metabolic alterations, but none of these explained associations between adiposity and CRC. More detailed metabolomic measures are likely needed to clarify the mechanistic pathways.
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| 19. |
- Carroll, Harriet A., et al.
(author)
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Effect of acute hypohydration on glycemic regulation in healthy adults : A randomized crossover trial
- 2019
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In: Journal of Applied Physiology. - : American Physiological Society. - 8750-7587 .- 1522-1601. ; 126:2, s. 422-430
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Journal article (peer-reviewed)abstract
- he aim of this study was to investigate the acute effect of hydration status on glycemic regulation in healthy adults and explore underlying mechanisms. In this randomized crossover trial, 16 healthy adults (8 men, 8 women) underwent an oral glucose tolerance test (OGTT) when hypohydrated and rehydrated after 4 days of pretrial standardization. One day before OGTT, participants were dehydrated for 1 h in a heat tent with subsequent fluid restriction (HYPO) or replacement (RE). The following day, an OGTT was performed with metabolic rate measurements and pre- and post-OGTT muscle biopsies. Peripheral quantitative computer tomography thigh scans were taken before and after intervention to infer changes in cell volume. HYPO (but not RE) induced 1.9% (SD 1.2) body mass loss, 2.9% (SD 2.7) cell volume reduction, and increased urinary hydration markers, serum osmolality, and plasma copeptin concentration (all P 0.007). Fasted serum glucose [HYPO 5.10 mmol/l (SD 0.42), RE 5.02 mmol/l (SD 0.40); P 0.327] and insulin [HYPO 27.1 pmol/l (SD 9.7), RE 27.6 pmol/l (SD 9.2); P 0.809] concentrations were similar between HYPO and RE. Hydration status did not alter the serum glucose (P 0.627) or insulin (P 0.200) responses during the OGTT. Muscle water content was lower before OGTT after HYPO compared with RE [761 g/kg wet wt (SD 13) vs. 772 g/kg wet wt (SD 18) RE] but similar after OGTT [HYPO 779 g/kg wet wt (SD 15) vs. RE 780 g/kg wet wt (SD 20); time P 0.011; trial time P 0.055]. Resting energy expenditure was similar between hydration states (stable between 1.21 and 5.94 kJ·kg 1 ·day 1 ; trial P 0.904). Overall, despite acute mild hypohydration increasing plasma copeptin concentrations and decreasing fasted cell volume and muscle water, we found no effect on glycemic regulation.
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| 20. |
- Eskelund, Christian Winther, et al.
(author)
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Detailed Long-Term Follow-Up of Patients Who Relapsed After the Nordic Mantle Cell Lymphoma Trials : MCL2 and MCL3
- 2021
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In: HemaSphere. - : Wolters Kluwer. - 2572-9241. ; 5:1
-
Journal article (peer-reviewed)abstract
- Mantle cell lymphoma (MCL) is an incurable disease with a highly variable clinical course. The prognosis after relapse is generally poor, and no standard of care exists. We investigated the postrelapse outcomes of 149 patients who were initially treated in the Nordic Lymphoma Group trials, MCL2 or MCL3, both representing intensive cytarabine-containing frontline regimens including autologous stem cell transplant. Patients with progression of disease before 24 months (POD24, n = 51, 34%) displayed a median overall survival of 6.6 months compared with 46 months for patients with later POD (n = 98, 66%; P < 0.001). MCL international prognostic index, cell proliferation marker, blastoid morphology, and TP53 mutations showed independent prognostic value irrespective of POD24, and in a combined, exploratory risk score, patients with 0, 1, 2-3, or 4-5 high-risk markers, respectively, displayed a 5-year overall survival of 62%, 39%, 31%, and 0%. By a comparison of median progression-free survival of the different salvage therapies in the relapse setting, bendamustine-rituximab was superior to all other combination chemotherapy regimens; however, it was also associated with longer responses to last line of therapy. Collectively, we confirm the prognostic impact of POD24 and highlight the relevance of other biomarkers, and we emphasize the importance of novel therapies for patients with high-risk features at first POD.
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| 21. |
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| 22. |
- Fanourgakis, George S., et al.
(author)
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Evaluation of global simulations of aerosol particle and cloud condensation nuclei number, with implications for cloud droplet formation
- 2019
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In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 19:13, s. 8591-8617
-
Journal article (peer-reviewed)abstract
- A total of 16 global chemistry transport models and general circulation models have participated in this study; 14 models have been evaluated with regard to their ability to reproduce the near-surface observed number concentration of aerosol particles and cloud condensation nuclei (CCN), as well as derived cloud droplet number concentration (CDNC). Model results for the period 2011-2015 are compared with aerosol measurements (aerosol particle number, CCN and aerosol particle composition in the submicron fraction) from nine surface stations located in Europe and Japan. The evaluation focuses on the ability of models to simulate the average across time state in diverse environments and on the seasonal and short-term variability in the aerosol properties. There is no single model that systematically performs best across all environments represented by the observations. Models tend to underestimate the observed aerosol particle and CCN number concentrations, with average normalized mean bias (NMB) of all models and for all stations, where data are available, of -24% and -35% for particles with dry diameters >50 and >120nm, as well as -36% and -34% for CCN at supersaturations of 0.2% and 1.0%, respectively. However, they seem to behave differently for particles activating at very low supersaturations (<0.1%) than at higher ones. A total of 15 models have been used to produce ensemble annual median distributions of relevant parameters. The model diversity (defined as the ratio of standard deviation to mean) is up to about 3 for simulated N3 (number concentration of particles with dry diameters larger than 3nm) and up to about 1 for simulated CCN in the extra-polar regions. A global mean reduction of a factor of about 2 is found in the model diversity for CCN at a supersaturation of 0.2% (CCN0.2) compared to that for N3, maximizing over regions where new particle formation is important. An additional model has been used to investigate potential causes of model diversity in CCN and bias compared to the observations by performing a perturbed parameter ensemble (PPE) accounting for uncertainties in 26 aerosol-related model input parameters. This PPE suggests that biogenic secondary organic aerosol formation and the hygroscopic properties of the organic material are likely to be the major sources of CCN uncertainty in summer, with dry deposition and cloud processing being dominant in winter. Models capture the relative amplitude of the seasonal variability of the aerosol particle number concentration for all studied particle sizes with available observations (dry diameters larger than 50, 80 and 120nm). The short-term persistence time (on the order of a few days) of CCN concentrations, which is a measure of aerosol dynamic behavior in the models, is underestimated on average by the models by 40% during winter and 20% in summer. In contrast to the large spread in simulated aerosol particle and CCN number concentrations, the CDNC derived from simulated CCN spectra is less diverse and in better agreement with CDNC estimates consistently derived from the observations (average NMB -13% and -22% for updraft velocities 0.3 and 0.6ms-1, respectively). In addition, simulated CDNC is in slightly better agreement with observationally derived values at lower than at higher updraft velocities (index of agreement 0.64 vs. 0.65). The reduced spread of CDNC compared to that of CCN is attributed to the sublinear response of CDNC to aerosol particle number variations and the negative correlation between the sensitivities of CDNC to aerosol particle number concentration (Nd=Na) and to updraft velocity (Nd=w). Overall, we find that while CCN is controlled by both aerosol particle number and composition, CDNC is sensitive to CCN at low and moderate CCN concentrations and to the updraft velocity when CCN levels are high. Discrepancies are found in sensitivities Nd=Na and Nd=w; models may be predisposed to be too "aerosol sensitive" or "aerosol insensitive" in aerosol-cloud-climate interaction studies, even if they may capture average droplet numbers well. This is a subtle but profound finding that only the sensitivities can clearly reveal and may explain intermodel biases on the aerosol indirect effect.
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| 23. |
- Fauchez, Thomas J., et al.
(author)
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The TRAPPIST-1 Habitable Atmosphere Intercomparison (THAI). III. Simulated Observables-the Return of the Spectrum
- 2022
-
In: The Planetary Science Journal. - : Institute of Physics Publishing (IOPP). - 2632-3338. ; 3:9
-
Journal article (peer-reviewed)abstract
- The TRAPPIST-1 Habitable Atmosphere Intercomparison (THAI) is a community project that aims to quantify how differences in general circulation models (GCMs) could impact the climate prediction for TRAPPIST-1e and, subsequently, its atmospheric characterization in transit. Four GCMs have participated in THAI: ExoCAM, LMD-Generic, ROCKE-3D, and the UM. This paper, focused on the simulated observations, is the third part of a trilogy, following the analysis of two land planet scenarios (Part I) and two aquaplanet scenarios (Part II). Here we show a robust agreement between the simulated spectra and the number of transits estimated to detect the land planet atmospheres. For the cloudy aquaplanet ones, a 5 sigma detection of CO2 could be achieved in about 10 transits if the atmosphere contains at least 1 bar of CO2. That number can vary by 41%-56% depending on the GCM used to predict the terminator profiles, principally due to differences in the cloud deck altitude, with ExoCAM and LMD-G producing higher clouds than ROCKE-3D and UM. Therefore, for the first time, this work provides "GCM uncertainty error bars" of similar to 50% that need to be considered in future analyses of transmission spectra. We also analyzed the intertransit spectral variability. Its magnitude differs significantly between the GCMs, but its impact on the transmission spectra is within the measurement uncertainties. THAI has demonstrated the importance of model intercomparison for exoplanets and also paved the way for a larger project to develop an intercomparison meta-framework, namely, the Climates Using Interactive Suites of Intercomparisons Nested for Exoplanet Studies.
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| 24. |
- Ghia, P., et al.
(author)
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Early stages in the ontogeny of small B-cell lymphomas : genetics and microenvironment
- 2017
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In: Journal of Internal Medicine. - : Wiley. - 0954-6820 .- 1365-2796. ; 282:5, s. 395-414
-
Journal article (peer-reviewed)abstract
- In this review, we focus on the mechanisms underlying lymphomagenesis in chronic lymphocytic leukaemia, follicular lymphoma, mantle cell lymphoma and splenic marginal zone lymphoma. The cells of origin of these small B-cell lymphomas are distinct, as are the characteristic chromosomal lesions and clinical courses. One shared feature is retention of expression of surface immunoglobulin. Analysis of this critical receptor reveals the point of differentiation reached by the cell of origin. Additionally, the sequence patterns of the immunoglobulin-variable domains can indicate a role for stimulants of the B-cell receptor before, during and after malignant transformation. The pathways driven via the B-cell receptor are now being targeted by specific kinase inhibitors with exciting clinical effects. To consider routes to pathogenesis, potentially offering earlier intervention, or to identify causative factors, genetic tools are being used to track pretransformation events and the early phases in lymphomagenesis. These methods are revealing that chromosomal changes are only one of the many steps involved, and that the influence of surrounding cells, probably multiple and variable according to tissue location, is required, both to establish tumours and to maintain growth and survival. Similarly, the influence of the tumour microenvironment may protect malignant cells from eradication by treatment, and the resulting minimal residual disease will eventually give rise to relapse. The common and different features of the four lymphomas will be summarized to show how normal B lymphocytes can be subverted to generate tumours, how these tumours evolve and how their weaknesses can be attacked by targeted therapies.
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| 25. |
- Ioannou, Leonidas G., et al.
(author)
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Occupational heat stress : Multi-country observations and interventions
- 2021
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In: International Journal of Environmental Research and Public Health. - : MDPI AG. - 1661-7827 .- 1660-4601. ; 18:12
-
Journal article (peer-reviewed)abstract
- Background: Occupational heat exposure can provoke health problems that increase the risk of certain diseases and affect workers’ ability to maintain healthy and productive lives. This study investigates the effects of occupational heat stress on workers’ physiological strain and labor productivity, as well as examining multiple interventions to mitigate the problem. Methods: We monitored 518 full work-shifts obtained from 238 experienced and acclimatized individuals who work in key industrial sectors located in Cyprus, Greece, Qatar, and Spain. Continuous core body temperature, mean skin temperature, heart rate, and labor productivity were collected from the beginning to the end of all work-shifts. Results: In workplaces where self-pacing is not feasible or very limited, we found that occupational heat stress is associated with the heat strain experienced by workers. Strategies focusing on hydration, work-rest cycles, and ventilated clothing were able to mitigate the physiological heat strain experienced by workers. Increasing mechanization enhanced labor productivity without increasing workers’ physiological strain. Conclusions: Empowering la-borers to self-pace is the basis of heat mitigation, while tailored strategies focusing on hydration, work-rest cycles, ventilated garments, and mechanization can further reduce the physiological heat strain experienced by workers under certain conditions.
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| 26. |
- Ioannou, Nikolaos, et al.
(author)
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Triggering interferon signaling in T cells with avadomide sensitizes CLL to anti-PD-L1 /PD-1 immunotherapy
- 2021
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In: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 137:2, s. 216-231
-
Journal article (peer-reviewed)abstract
- Cancer treatment has been transformed by checkpoint blockade therapies, with the highest anti-tumor activity of anti-programmed death 1 (PD-1) antibody therapy seen in Hodgkin lymphoma. Disappointingly, response rates have been low in the non-Hodgkin lymphomas, with no activity seen in relapsed/refractory chronic lymphocytic leukemia (CLL) with PD-1 blockade. Thus, identifying more powerful combination therapy is required for these patients. Here, we preclinically demonstrate enhanced anti-CLL activity following combinational therapy with anti-PD-1 or anti-PD-1 ligand (PD-L1) and avadomide, a cereblon E3 ligase modulator (CELMoD). Avadomide induced type I and II interferon (IFN) signaling in patient T cells, triggering a feedforward cascade of reinvigorated T-cell responses. Immune modeling assays demonstrated that avadomide stimulated T-cell activation, chemokine expression, motility and lytic synapses with CLL cells, as well as IFN-inducible feedback inhibition through upregulation of PD-L1. Patient-derived xenograft tumors treated with avadomide were converted to CD8(+) T cell-inflamed tumor microenvironments that responded to anti-PD-L1/PD-1-based combination therapy. Notably, clinical analyses showed increased PD-L1 expression on T cells, as well as intratumoral expression of chemokine signaling genes in B-cell malignancy patients receiving avadomide-based therapy. These data of overcoming a low inflammatory T-cell state to successfully sensitize CLL to checkpoint illustrate the importance blockade-based combination therapy.
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| 27. |
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| 28. |
- Lappalainen, Hanna K., et al.
(author)
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Pan-Eurasian Experiment (PEEX) : towards a holistic understanding of the feedbacks and interactions in the land-atmosphere-ocean-society continuum in the northern Eurasian region
- 2016
-
In: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 16:22, s. 14421-14461
-
Journal article (peer-reviewed)abstract
- The northern Eurasian regions and Arctic Ocean will very likely undergo substantial changes during the next decades. The Arctic-boreal natural environments play a crucial role in the global climate via albedo change, carbon sources and sinks as well as atmospheric aerosol production from biogenic volatile organic compounds. Furthermore, it is expected that global trade activities, demographic movement, and use of natural resources will be increasing in the Arctic regions. There is a need for a novel research approach, which not only identifies and tackles the relevant multi-disciplinary research questions, but also is able to make a holistic system analysis of the expected feedbacks. In this paper, we introduce the research agenda of the Pan-Eurasian Experiment (PEEX), a multi-scale, multi-disciplinary and international program started in 2012 (https://www.atm.helsinki.fi/peex/). PEEX sets a research approach by which large-scale research topics are investigated from a system perspective and which aims to fill the key gaps in our understanding of the feedbacks and interactions between the land-atmosphereaquatic-society continuum in the northern Eurasian region. We introduce here the state of the art for the key topics in the PEEX research agenda and present the future prospects of the research, which we see relevant in this context.
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| 29. |
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| 30. |
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| 31. |
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| 32. |
- Rothwell, Joseph A., et al.
(author)
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Circulating amino acid levels and colorectal cancer risk in the European Prospective Investigation into Cancer and Nutrition and UK Biobank cohorts
- 2023
-
In: BMC Medicine. - : BioMed Central (BMC). - 1741-7015. ; 21:1
-
Journal article (peer-reviewed)abstract
- Background: Amino acid metabolism is dysregulated in colorectal cancer patients; however, it is not clear whether pre-diagnostic levels of amino acids are associated with subsequent risk of colorectal cancer. We investigated circulating levels of amino acids in relation to colorectal cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC) and UK Biobank cohorts.Methods: Concentrations of 13-21 amino acids were determined in baseline fasting plasma or serum samples in 654 incident colorectal cancer cases and 654 matched controls in EPIC. Amino acids associated with colorectal cancer risk following adjustment for the false discovery rate (FDR) were then tested for associations in the UK Biobank, for which measurements of 9 amino acids were available in 111,323 participants, of which 1221 were incident colorectal cancer cases.Results: Histidine levels were inversely associated with colorectal cancer risk in EPIC (odds ratio [OR] 0.80 per standard deviation [SD], 95% confidence interval [CI] 0.69–0.92, FDR P-value=0.03) and in UK Biobank (HR 0.93 per SD, 95% CI 0.87–0.99, P-value=0.03). Glutamine levels were borderline inversely associated with colorectal cancer risk in EPIC (OR 0.85 per SD, 95% CI 0.75–0.97, FDR P-value=0.08) and similarly in UK Biobank (HR 0.95, 95% CI 0.89–1.01, P=0.09) In both cohorts, associations changed only minimally when cases diagnosed within 2 or 5 years of follow-up were excluded.Conclusions: Higher circulating levels of histidine were associated with a lower risk of colorectal cancer in two large prospective cohorts. Further research to ascertain the role of histidine metabolism and potentially that of glutamine in colorectal cancer development is warranted.
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| 33. |
- Rothwell, Joseph A., et al.
(author)
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Metabolic signatures of healthy lifestyle patterns and colorectal cancer risk in a European cohort
- 2022
-
In: Clinical Gastroenterology and Hepatology. - : Elsevier. - 1542-3565 .- 1542-7714. ; 20:5, s. e1061-e1082
-
Journal article (peer-reviewed)abstract
- Background & Aims: Colorectal cancer risk can be lowered by adherence to the World Cancer Research Fund/American Institute for Cancer Research (WCRF/AICR) guidelines. We derived metabolic signatures of adherence to these guidelines and tested their associations with colorectal cancer risk in the European Prospective Investigation into Cancer and Nutrition cohort.Methods: Scores reflecting adherence to the WCRF/AICR recommendations (scale, 1–5) were calculated from participant data on weight maintenance, physical activity, diet, and alcohol among a discovery set of 5738 cancer-free European Prospective Investigation into Cancer and Nutrition participants with metabolomics data. Partial least-squares regression was used to derive fatty acid and endogenous metabolite signatures of the WCRF/AICR score in this group. In an independent set of 1608 colorectal cancer cases and matched controls, odds ratios (ORs) and 95% CIs were calculated for colorectal cancer risk per unit increase in WCRF/AICR score and per the corresponding change in metabolic signatures using multivariable conditional logistic regression.Results: Higher WCRF/AICR scores were characterized by metabolic signatures of increased odd-chain fatty acids, serine, glycine, and specific phosphatidylcholines. Signatures were inversely associated more strongly with colorectal cancer risk (fatty acids: OR, 0.51 per unit increase; 95% CI, 0.29–0.90; endogenous metabolites: OR, 0.62 per unit change; 95% CI, 0.50–0.78) than the WCRF/AICR score (OR, 0.93 per unit change; 95% CI, 0.86–1.00) overall. Signature associations were stronger in male compared with female participants.Conclusions: Metabolite profiles reflecting adherence to WCRF/AICR guidelines and additional lifestyle or biological risk factors were associated with colorectal cancer. Measuring a specific panel of metabolites representative of a healthy or unhealthy lifestyle may identify strata of the population at higher risk of colorectal cancer.
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| 34. |
- Sarakinos, Kostas, et al.
(author)
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Ionized physical vapor deposited Al(2)O(3) films : Does subplantation favor formation of alpha-Al(2)O(3)?
- 2010
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In: Physica Status Solidi. Rapid Research Letters. - : Wiley-VCH Verlag Berlin. - 1862-6254 .- 1862-6270. ; 4:7, s. 154-156
-
Journal article (peer-reviewed)abstract
- The broad energy distributions of the condensing particles typically encountered in ion assisted vapor deposition techniques are often a drawback when attempting to understand the effect of the energetic bombardment on the film properties. In the current study, a monoenergetic Al beam generated by a filtered cathodic arc discharge is employed for the deposition of alumina (Al(2)O(3)) films at well defined AI ion energies between 4 eV and 200 eV at a substrate temperature of 720 degrees C. Structural analysis shows that Al energies of 40 eV or larger favor the formation of the thermodynamically stable zeta-Al(2)O(3) phase at the expense of other metastable Al(2)O(3) polymorphs. The well defined ion energies are used as input for Monte-Carlo based simulations of the ion surface interactions. The results of these simulations reveal that the increase of the Al(+) ion energy leads to an increase in the fraction of ions subplanted into the growing film. These findings underline the previously not considered role of subsurface processes on the phase formation of ionized physical vapor deposited Al(2)O(3) films.
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| 35. |
- Sarakinos, Kostas, et al.
(author)
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On the phase formation of sputtered hafnium oxide and oxynitride films
- 2010
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In: Journal of Applied Physics. - : American Institute of Physics (AIP). - 0021-8979 .- 1089-7550. ; 108:1, s. 014904-
-
Journal article (peer-reviewed)abstract
- Hafnium oxynitride films are deposited from a Hf target employing direct current magnetron sputtering in an Ar-O(2)-N(2) atmosphere. It is shown that the presence of N(2) allows for the stabilization of the transition zone between the metallic and the compound sputtering mode enabling deposition of films at well defined conditions of target coverage by varying the O(2) partial pressure. Plasma analysis reveals that this experimental strategy facilitates control over the flux of the O(-) ions which are generated on the oxidized target surface and accelerated by the negative target potential toward the growing film. An arrangement that enables film growth without O(-) ion bombardment is also implemented. Moreover, stabilization of the transition sputtering zone and control of the O(-) ion flux without N(2) addition is achieved employing high power pulsed magnetron sputtering. Structural characterization of the deposited films unambiguously proves that the phase formation of hafnium oxide and hafnium oxynitride films with the crystal structure of HfO(2) is independent from the O(-) bombardment conditions. Experimental and theoretical data indicate that the presence of vacancies and/or the substitution of O by N atoms in the nonmetal sublattice favor the formation of the cubic and/or the tetragonal HfO(2) crystal structure at the expense of the monoclinic HfO(2) one.
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| 36. |
- Sergeev, Denis E., et al.
(author)
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The TRAPPIST-1 Habitable Atmosphere Intercomparison (THAI). II. Moist Cases-The Two Waterworlds
- 2022
-
In: The Planetary Science Journal. - : IOP Publishing Ltd. - 2632-3338. ; 3:9
-
Journal article (peer-reviewed)abstract
- To identify promising exoplanets for atmospheric characterization and to make the best use of observational data, a thorough understanding of their atmospheres is needed. Three-dimensional general circulation models (GCMs) are one of the most comprehensive tools available for this task and will be used to interpret observations of temperate rocky exoplanets. Due to parameterization choices made in GCMs, they can produce different results, even for the same planet. Employing four widely used exoplanetary GCMs-ExoCAM, LMD-G, ROCKE-3D, and the UM-we continue the TRAPPIST-1 Habitable Atmosphere Intercomparison by modeling aquaplanet climates of TRAPPIST-1e with a moist atmosphere dominated by either nitrogen or carbon dioxide. Although the GCMs disagree on the details of the simulated regimes, they all predict a temperate climate with neither of the two cases pushed out of the habitable state. Nevertheless, the intermodel spread in the global mean surface temperature is nonnegligible: 14 K and 24 K in the nitrogen- and carbon dioxide-dominated case, respectively. We find substantial intermodel differences in moist variables, with the smallest amount of clouds in LMD-Generic and the largest in ROCKE-3D. ExoCAM predicts the warmest climate for both cases and thus has the highest water vapor content and the largest amount and variability of cloud condensate. The UM tends to produce colder conditions, especially in the nitrogen-dominated case due to a strong negative cloud radiative effect on the day side of TRAPPIST-1e. Our study highlights various biases of GCMs and emphasizes the importance of not relying solely on one model to understand exoplanet climates.
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| 37. |
- Stefanis, Leonidas, et al.
(author)
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How is alpha-synuclein cleared from the cell?
- 2019
-
In: Journal of Neurochemistry. - : Wiley. - 0022-3042 .- 1471-4159. ; 150:5, s. 577-590
-
Research review (peer-reviewed)abstract
- The levels and conformers of alpha-synuclein are critical in the pathogenesis of Parkinson's Disease and related synucleinopathies. Homeostatic mechanisms in protein degradation and secretion have been identified as regulators of alpha-synuclein at different stages of its intracellular trafficking and transcellular propagation. Here we review pathways involved in the removal of various forms of alpha-synuclein from both the intracellular and extracellular environment. Proteasomes and lysosomes are likely to play complementary roles in the removal of intracellular alpha-synuclein species, in a manner that depends on alpha-synuclein post-translational modifications. Extracellular alpha-synuclein is cleared by extracellular proteolytic enzymes, or taken up by neighboring cells, especially microglia and astrocytes, and degraded within lysosomes. Exosomes, on the other hand, represent a vehicle for egress of excess burden of the intracellular protein, potentially contributing to the transfer of alpha-synuclein between cells. Dysfunction in any one of these clearance mechanisms, or a combination thereof, may be involved in the initiation or progression of Parkinson's disease, whereas targeting these pathways may offer an opportunity for therapeutic intervention. (Figure presented.).
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| 38. |
- Szatmari, Peter, et al.
(author)
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Mapping autism risk loci using genetic linkage and chromosomal rearrangements.
- 2007
-
In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 39:3, s. 319-328
-
Journal article (peer-reviewed)abstract
- Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,168 families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.
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| 39. |
- Turbet, Martin, et al.
(author)
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The TRAPPIST-1 Habitable Atmosphere Intercomparison (THAI). I. Dry Cases-The Fellowship of the GCMs
- 2022
-
In: The Planetary Science Journal. - : IOP Publishing Ltd. - 2632-3338. ; 3:9
-
Journal article (peer-reviewed)abstract
- With the commissioning of powerful, new-generation telescopes such as the James Webb Space Telescope (JWST) and the ground-based Extremely Large Telescopes, the first characterization of a high molecular weight atmosphere around a temperate rocky exoplanet is imminent. Atmospheric simulations and synthetic observables of target exoplanets are essential to prepare and interpret these observations. Here we report the results of the first part of the TRAPPIST-1 Habitable Atmosphere Intercomparison (THAI) project, which compares 3D numerical simulations performed with four state-of-the-art global climate models (ExoCAM, LMD-Generic, ROCKE-3D, Unified Model) for the potentially habitable target TRAPPIST-1e. In this first part, we present the results of dry atmospheric simulations. These simulations serve as a benchmark to test how radiative transfer, subgrid-scale mixing (dry turbulence and convection), and large-scale dynamics impact the climate of TRAPPIST-1e and consequently the transit spectroscopy signature as seen by JWST. To first order, the four models give results in good agreement. The intermodel spread in the global mean surface temperature amounts to 7 K (6 K) for the N-2-dominated (CO2-dominated) atmosphere. The radiative fluxes are also remarkably similar (intermodel variations less than 5%), from the surface (1 bar) up to atmospheric pressures similar to 5 mbar. Moderate differences between the models appear in the atmospheric circulation pattern (winds) and the (stratospheric) thermal structure. These differences arise between the models from (1) large-scale dynamics, because TRAPPIST-1e lies at the tipping point between two different circulation regimes (fast and Rhines rotators) in which the models can be alternatively trapped, and (2) parameterizations used in the upper atmosphere such as numerical damping.
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| 40. |
- van Duijnhoven, Fränzel J B, et al.
(author)
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Blood lipid and lipoprotein concentrations and colorectal cancer risk in the European Prospective Investigation into Cancer and Nutrition
- 2011
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In: Gut. - London : BMJ Publishing. - 0017-5749 .- 1468-3288. ; 60:8, s. 1094-1102
-
Journal article (peer-reviewed)abstract
- OBJECTIVE: To examine the association between serum concentrations of total cholesterol, high density lipoprotein cholesterol (HDL), low density lipoprotein cholesterol, triglycerides, apolipoprotein A-I (apoA), apolipoprotein B and the incidence of colorectal cancer (CRC). DESIGN: Nested case-control study. SETTING: The study was conducted within the European Prospective Investigation into Cancer and Nutrition (EPIC), a cohort of more than 520,000 participants from 10 western European countries. PARTICIPANTS: 1238 cases of incident CRC, which developed after enrolment into the cohort, were matched with 1238 controls for age, sex, centre, follow-up time, time of blood collection and fasting status. MAIN OUTCOME MEASURES: Serum concentrations were quantitatively determined by colorimetric and turbidimetric methods. Dietary and lifestyle data were obtained from questionnaires. Conditional logistic regression models were used to estimate incidence rate ratios (RRs) and 95% CIs which were adjusted for height, weight, smoking habits, physical activity, education, consumption of fruit, vegetables, meat, fish, alcohol, fibre and energy. RESULTS: After adjustments, the concentrations of HDL and apoA were inversely associated with the risk of colon cancer (RR for 1 SD increase of 16.6 mg/dl in HDL and 32.0 mg/dl in apoA of 0.78 (95% CI 0.68 to 0.89) and 0.82 (95% CI 0.72 to 0.94), respectively). No association was observed with the risk of rectal cancer. Additional adjustment for biomarkers of systemic inflammation, insulin resistance and oxidative stress or exclusion of the first 2 years of follow-up did not influence the association between HDL and risk of colon cancer. CONCLUSIONS: These findings show that high concentrations of serum HDL are associated with a decreased risk of colon cancer. The mechanism behind this association needs further elucidation.
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| 41. |
- Vardi, A., et al.
(author)
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Restrictions in the T-cell repertoire of chronic lymphocytic leukemia : high-throughput immunoprofiling supports selection by shared antigenic elements
- 2017
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In: Leukemia. - : Springer Science and Business Media LLC. - 0887-6924 .- 1476-5551. ; 31:7, s. 1555-1561
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Journal article (peer-reviewed)abstract
- Immunoglobulin (IG) gene repertoire restrictions strongly support antigen selection in the pathogenesis of chronic lymphocytic leukemia (CLL). Given the emerging multifarious interactions between CLL and bystander T cells, we sought to determine whether antigen(s) are also selecting T cells in CLL. We performed a large-scale, next-generation sequencing (NGS) study of the T-cell repertoire, focusing on major stereotyped subsets representing CLL subgroups with undisputed antigenic drive, but also included patients carrying non-subset IG rearrangements to seek for T-cell immunogenetic signatures ubiquitous in CLL. Considering the inherent limitations of NGS, we deployed bioinformatics algorithms for qualitative curation of T-cell receptor rearrangements, and included multiple types of controls. Overall, we document the clonal architecture of the T-cell repertoire in CLL. These T-cell clones persist and further expand overtime, and can be shared by different patients, most especially patients belonging to the same stereotyped subset. Notably, these shared clonotypes appear to be disease-specific, as they are found in neither public databases nor healthy controls. Altogether, these findings indicate that antigen drive likely underlies T-cell expansions in CLL and may be acting in a CLL subset-specific context. Whether these are the same antigens interacting with the malignant clone or tumor-derived antigens remains to be elucidated.
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| 42. |
- Xochelli, Aliki, et al.
(author)
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Clonal B-cell lymphocytosis exhibiting immunophenotypic features consistent with a marginal-zone origin : is this a distinct entity?
- 2014
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In: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 123:8, s. 1199-1206
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Journal article (peer-reviewed)abstract
- The biological and clinical significance of a clonal B-cell lymphocytosis with an immunophenotype consistent with marginal-zone origin (CBL-MZ) is poorly understood. We retrospectively evaluated 102 such cases with no clinical evidence to suggest a concurrent MZ lymphoma. Immunophenotyping revealed a clonal B-cell population with Matutes score <= 2 in all cases; 19/102 were weakly CD5 positive and all 35 cases tested expressed CD49d. Bone marrow biopsy exhibited mostly mixed patterns of small B-lymphocytic infiltration. A total of 48/66 (72.7%) cases had an abnormal karyotype. Immunogenetics revealed overusage of the IGHV4-34 gene and somatic hypermutation in 71/79 (89.8%) IGHV-IGHD-IGHJ gene rearrangements. With a median follow-up of 5 years, 85 cases remain stable (group A), whereas 17 cases (group B) progressed, of whom 15 developed splenomegaly. The clonal B-cell count, degree of marrow infiltration, immunophenotypic, or immunogenetic findings at diagnosis did not distinguish between the 2 groups. However, deletions of chromosome 7q were confined to group A and complex karyotypes were more frequent in group B. Although CBL-MZ may antedate SMZL/SLLU, most cases remain stable over time. These cases, not readily classifiable within the World Heath Organization classification, raise the possibility that CBL-MZ should be considered as a new provisional entity within the spectrum of clonal MZ disorders.
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