Browsing by Subject "PHASE"

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  • Kassamakov, Ivan; Lecler, Sylvain; Nolvi, Anton; Leong-Hoi, Audrey; Montgomery, Paul; Haeggström, Edward (2017)
    We present quantitative three dimensional images of grooves on a writable Blu-ray Disc based on a single objective Mirau type interferometric microscope, enhanced with a microsphere which is considered as a photonic nanojet source. Along the optical axis the resolution of this microsphere assisted interferometry system is a few nanometers while the lateral resolution is around 112 nm. To understand the physical phenomena involved in this kind of imaging we have modelled the interaction between the photonic jet and the complex disc surface. Agreement between simulation and experimental results is demonstrated. We underline that although the ability of the microsphere to generate a photonic nanojet does not alone explain the resolution of the interferometer, the nanojet can be used to try to understand the imaging process. To partly explain the lateral super-resolution, the potential role of coherence is illustrated. The presented modality may have a large impact on many fields from bio-medicine to nanotechnology.
  • Kuhle, J.; Hardmeier, M.; Disanto, G.; Gugleta, K.; Ecsedi, M.; Lienert, C.; Amato, M. P.; Baum, K.; Buttmann, M.; Bayas, A.; Brassat, D.; Brochet, B.; Confavreux, C.; Edan, G.; Färkkilä, Markus; Fredrikson, S.; Frontoni, M.; D'Hooghe, M.; Hutchinson, M.; De Keyser, J.; Kieseier, B. C.; Kuempfel, T.; Rio, J.; Polman, C.; Roullet, E.; Stolz, C.; Vass, K.; Wandinger, K. P.; Kappos, L.; European Long Term Follow Up Study (2016)
    Objectives: To explore long-term effects of treatment and prognostic relevance of variables assessed at baseline and during the European secondary progressive multiple sclerosis (SPMS) trial of interferon beta 1b (IFNB-1b). Methods: We assessed 362 patients (60% female; median age 41 years; Expanded Disability Status Scale (EDSS): 5.5; 51% randomized to IFNB-1b) for their EDSS and treatment history after 10 years. Non-parametric analysis of covariance (ANCOVA) and multivariate linear regression models were applied. Results: Median EDSS was 6.0 at the end of the randomized controlled trial (RCT), in the IFNB-1b and placebo groups, and 7.0 in long-term follow-up patients (those receiving IFNB-1b in the RCT were 6.5 and those receiving placebo in the RCT were 7.0; p = 0.086). 24 patients (6.6%) were deceased. The EDSS at baseline and the EDSS change during the RCT were the most important predictors of the EDSS 10 years later (partial R-2: 0.47). The ability to predict changes in EDSS 10 years after the RCT was limited (R-2: 0.12). Magnetic resonance imaging (MRI) measures remained in the predictive models, but explained <5% of the variability. Conclusions: The results from this analysis did not provide convincing evidence to support a favorable long-term outcome in those patients allocated IFNB-1b during the RCT, in our SPMS cohort. The progressive stage of the disease remains largely unpredictable by clinical and conventional MRI measures, so better prognostic markers are needed.
  • Zappa, Emilio; Dykeman, Eric C.; Geraets, James A.; Twarock, Reidun (2016)
    In this paper we describe a group theoretical approach to the study of structural transitions of icosahedral quasicrystals and point arrays. We apply the concept of Schur rotations, originally proposed by Kramer, to the case of aperiodic structures with icosahedral symmetry; these rotations induce a rotation of the physical and orthogonal spaces invariant under the icosahedral group, and hence, via the cut-and-project method, a continuous transformation of the corresponding model sets. We prove that this approach allows for a characterisation of such transitions in a purely group theoretical framework, and provide explicit computations and specific examples. Moreover, we prove that this approach can be used in the case of finite point sets with icosahedral symmetry, which have a wide range of applications in carbon chemistry (fullerenes) and biology (viral capsids).
  • Costa de Oliveira, Regiane; Soares Pontes, Gemilson; Kostyuk, Aleksandr; Coutinho Camargo, Gabriel B.; Dhyani, Anamika; Shvydenko, Tetiana; Shvydenko, Kostiantyn; Grafov, Andriy (2020)
    Cancer still remains a major public health concern around the world and the search for new potential antitumor molecules is essential for fighting the disease. This study evaluated the anticancer and immunomodulatory potential of the newly synthetized ellipticine derivate: sodium bromo-5,11-dimethyl-6H-pyrido[4,3-b]carbazole-7-sulfonate (Br-Ell-SO3Na). It was prepared by the chlorosulfonation of 9-bromoellipticine. The ellipticine-7-sulfonic acid itself is not soluble, but its saponification with sodium hydroxide afforded a water-soluble sodium salt. The cytotoxicity of Br-Ell-SO3Na was tested against cancerous (K562 cell line) and non-cancerous cells (Vero cell line and human peripheral blood mononuclear cells (PBMC)) using a Methylthiazoletetrazolium (MTT) assay. Cell cycle arrest was assessed by flow cytometry and the immunomodulatory activity was analyzed through an enzyme-linked immunosorbent assay (ELISA)(.) The results showed that the Br-Ell-SO3Na molecule has specific anticancer activity (IC50 = 35 mu M) against the K562 cell line, once no cytotoxicity effect was verified against non-cancerous cells. Cell cycle analysis demonstrated that K562 cells treated with Br-Ell-SO3Na were arrested in the phase S. Moreover, the production of IL-6 increased and the expression of IL-8 was inhibited in the human PBMC treated with Br-Ell-SO3Na. The results demonstrated that Br-Ell-SO3Na is a promising anticancer molecule attested by its noteworthy activity against the K562 tumor cell line and immunomodulatory activity in human PBMC cells.
  • Merikanto, Ilona; Lahti, Tuuli; Seitsalo, Seppo; Kronholm, Erkki; Laatikainen, Tiina; Peltonen, Markku; Vartiainen, Erkki; Partonen, Timo (2014)
    Earlier studies have revealed that the more the preference to schedule daily activities towards the evening hours is, the higher the odds for a range of health hazards are. Therefore, we wanted to analyze, whether the behavioral trait of morningness-eveningness is associated with articular and spinal diseases or those with musculoskeletal disorders. Participants (n=6089), as part of the National FINRISK 2007 Study, were derived from the general population, aged 25 to 74 years, living in Finland. Chronotype was assessed based on six items from the original Horne-Ostberg Morningness-Eveningness Questionnaire. Information about risk factors and the diagnoses of articular and spinal diseases were based on the self-reported information. Our results suggest that Evening-types have higher odds for articular and spinal diseases as compared with Morning-types, and this risk is heightened especially regarding spinal disease and backache (odds ratios of 1.8 to 2.1, and 1.6 to 1.8, respectively) and remains significant after controlling for the sex, age, education, civil status, physical activity, alcohol use, and smoking, and additionally for the body-mass index, insufficient sleep, or depressive symptoms.
  • Toivola, Martta; Prisle, Nonne L.; Elm, Jonas; Waxman, Eleanor M.; Volkamer, Rainer; Kurten, Theo (2017)
    We have used COSMO-RS, a method combining quantum chemistry with statistical thermodynamics, to compute Setschenow constants (K-S) for a large array of organic solutes and salts. These comprise both atmospherically relevant solute-salt combinations, as well as systems for which experimental data are available. In agreement with previous studies on single salts, the Setschenow constants predicted by COSMO-RS (as implemented in the COSMOTherm program) are generally too large compared to experiments. COSMOTherm overpredicts salting out (positive K-S), and/or underpredicts salting in (negative K-S). For ammonium and sodium salts, K-S values are larger for oxalates and sulfates, and smaller for chlorides and bromides. For chloride and bromide salts, K-S values usually increase with decreasing size of the cation, along the series Pr4N+ <Et4N+ <Me4N+
  • Riva, Matthieu; Heikkinen, Liine; Bell, David M.; Peräkylä, Otso; Zha, Qiaozhi; Rissanen, Matti; Imre, D.; Petäjä, Tuukka; Thornton, Joel; Zelenyuk, Alla; Ehn, Mikael (2019)
    Secondary organic aerosol (SOA) is known to impact both climate and air quality, yet molecular-level composition measurements remain challenging, hampering our understanding of SOA formation and evolution. Here, we reveal the importance of underestimated reaction pathways for the (trans) formation of SOA from monoterpenes, one of the largest SOA precursors globally. Utilizing mass spectrometric techniques to achieve a comprehensive characterization of molecular-level changes in the SOA, we were able to link the appearance of high-molecular weight (HMW) organic molecules to the concentration and level of neutralization of particulate sulfate. Interestingly, this oligomerization coincided with a decrease of highly oxygenated molecules (HOMs). Our findings highlight the role of particle-phase processing, and the underestimated importance of sulfate aerosol for monoterpene-SOA formation. The observations of these processes directly in the atmosphere reveal the need to account for the formation of HMW oligomers to fully understand the physicochemical properties of organic aerosol.
  • Pätilä, Tommi; Miyagawa, Shigeru; Imanishi, Yukiko; Fukushima, Satsuki; Siltanen, Antti; Mervaala, Eero; Kankuri, Esko; Harjula, Ari; Sawa, Yoshiki (2015)
    Although cell therapy of the failing heart by intramyocardial injections of myoblasts to results in regenerative benefit, it has also been associated with undesired and prospectively fatal arrhythmias. We hypothesized that intramyocardial injections of myoblasts could enhance inflammatory reactivity and facilitate electrical cardiac abnormalities that can be reduced by epicardial myoblast sheet delivery. In a rat model of ischemic heart failure, myoblast therapy either by intramyocardial injections or epicardial cell sheets was given 2 weeks after occlusion of the coronary artery. Ventricular premature contractions (VPCs) were assessed, using an implanted three-lead electrocardiograph at 1, 7, and 14 days after therapy, and 16-point epicardial electropotential mapping (EEPM) was used to evaluate ventricular arrhythmogenicity under isoproterenol stress. Cardiac functioning was assessed by echocardiography. Both transplantation groups showed therapeutic benefit over sham therapy. However, VPCs were more frequent in the Injection group on day 1 and day 14 after therapy than in animals receiving epicardial or sham therapy (p <0.05 and p <0.01, respectively). EEPM under isoproterenol stress showed macroreentry at the infarct border area, leading to ventricular tachycardias in the Injection group, but not in the myoblast sheet- or sham-treated groups (p = 0.045). Both transplantation types modified the myocardial cytokine expression profile. In animals receiving epicardial myoblast therapy, selective reductions in the expressions of interferon gamma, interleukin (IL)-1 beta and IL12 were observed, accompanied by reduced infiltration of inflammatory CD11b- and CD68-positive leukocytes, compared with animals receiving myoblasts as intramyocardial injections. Intramyocardial myoblast delivery was associated with enhanced inflammatory and immunomodulatory reactivity and increased frequency of VPCs. In comparison to intramyocardial injection, the epicardial route may serve as the preferred method of skeletal myoblast transplantation to treat heart failure.
  • Ruuth, Riikka; Kuusela, Linda; Mäkelä, Teemu; Melkas, Susanna; Korvenoja, Antti (2019)
    Aim and scope: A Gradient Echo Plural Contrast Imaging technique (GEPCI) is a post-processing method, which can be used to obtain quantitative T2* values and generate multiple synthetic contrasts from a single acquisition. However, scan duration and image reconstruction from k-space data present challenges in a clinical workflow. This study aimed at optimizing image reconstruction and acquisition duration to facilitate a post-processing method for synthetic image contrast creation in clinical settings. Materials and methods: This study consists of tests using the American College of Radiology (ACR) image quality phantom, two healthy volunteers, four mild traumatic brain injury patients and four small vessel disease patients. The measurements were carried out on a 3.0 T scanner with multiple echo times. Reconstruction from k-space data and DICOM data with two different coil-channel combination modes were investigated. Partial Fourier techniques were tested to optimize the scanning time. Conclusions: Sum of squares coil-channel combination produced artifacts in phase images, but images created with adaptive combination were artifact-free. The voxel-wise median signed difference of T2* between the vendor's adaptive channel combination and k-space reconstruction modes was 2.9 +/- 0.7 ms for white matter and 4.5 +/- 0.6 ms for gray matter. Relative white matter/gray matter contrast of all synthetic images and contrast-to-noise ratio of synthetic T1-weighted images were almost equal between reconstruction modes. Our results indicate that synthetic contrasts can be generated from the vendor's DICOM data with the adaptive combination mode without affecting the quantitative T2* values or white matter/gray matter contrast.
  • Stepien, Piotr; Augustyn, Bozena; Poojari, Chetan; Galan, Wojciech; Polit, Agnieszka; Vattulainen, Ilpo; Wisnieska-Becker, Anna; Rog, Tomasz (2020)
    Lipid nanodiscs are macromolecular assemblies, where a scaffold protein is wrapped around a nanosized disc of a lipid bilayer, thus protecting the hydrocarbon chains at the disc edges from unfavorable interactions with water. These nanostructures have numerous applications in, e.g., nanotechnology and pharmaceutics, and in investigations of membrane proteins. Here, we present results based on atomistic molecular dynamics simulations combined with electron paramagnetic spectroscopy measurements on the structure and dynamics of lipids in single-component nanodiscs. Our data highlight the existence of three distinctly different lipid fractions: central lipids residing in the center of a nanodisc, boundary lipids in direct contact with a scaffold protein, and intermediate lipids between these two regions. The central lipids are highly ordered and characterized by slow diffusion. In this part of the nanodisc, the membrane is the thickest and characterized by a gel-like or liquid-ordered phase, having features common to cholesterol-rich membranes. The boundary lipids in direct contact with the scaffold protein turned out to be less ordered and characterized by faster diffusion, and they remained in the liquid-disordered phase even at temperatures that were somewhat below the main phase transition temperature (Tm). The enthalpies associated with the central-boundary and central-intermediate transitions were similar to those observed for lipids going through the main phase transition. Overall, the study reveals lipid nanodiscs to be characterized by a complex internal structure, which is expected to influence membrane proteins placed in nanodiscs.
  • George, Harriet E.; Rodger, Craig J.; Clilverd, Mark A.; Cresswell-Moorcock, Kathy; Brundell, James B.; Thomson, Neil R. (2019)
    A technique for analyzing very low frequency (VLF) radiowave signals is investigated in order to achieve rapid, real-time detection of large solar flares, through the monitoring of changes in VLF radio signal propagation conditions. The reliability of the use of VLF phase and amplitude perturbations to determine the X-ray fluxes involved during 10 large solar flare events (>X1) is examined. Linear regression analysis of signals from the NPM transmitter in Hawaii, received at Arrival Heights, Scott Base, Antarctica, over the years 2011-2015 shows that VLF phase perturbations during large solar flares have a 1.5-3 times lower mean square error when modeling the long wavelength X-ray fluxes than the equivalent short wavelength fluxes. The use of VLF amplitude observations to determine long or short wavelength X-ray flux levels have a 4-10 times higher mean square error than when using VLF phase. Normalized linear regression analysis identifies VLF phase as the most important parameter in the regression, followed by solar zenith angle at the midpoint of the propagation path, then the initial solar X-ray flux level (from 5 min before the impact of the solar flare), with F10.7 cm flux from the day beforehand providing the least important contribution. Transmitter phase measurements are more difficult to undertake than amplitude. However, networks of VLF receivers already exist which include the high quality phase capability required for such a nowcasting product. Such narrowband VLF data can be a redundant source of flare monitoring if satellite data is not available.
  • Montonen, Risto; Kassamakov, Ivan; Lehmann, Peter; Österberg, Kenneth; Haeggström, Edward (2018)
    The group refractive index is important in length calibration of Fourier domain interferometers by transparent transfer standards. We demonstrate accurate group refractive index quantification using a Fourier domain short coherence Sagnac interferometer. Because of a justified linear length calibration function, the calibration constants cancel out in the evaluation of the group refractive index, which is then obtained accurately from two uncalibrated lengths. Measurements of two standard thickness coverslips revealed group indices of 1.5426 +/- 0.0042 and 1.5434 +/- 0.0046, with accuracies quoted at the 95% confidence level. This agreed with the dispersion data of the coverslip manufacturer and therefore validates our method. Our method provides a sample specific and accurate group refractive index quantification using the same Fourier domain interferometer that is to be calibrated for the length. This reduces significantly the requirements of the calibration transfer standard. (C) 2018 Optical Society of America
  • Vilen, M.; Kankainen, A.; Baczyk, P.; Canete, L.; Dobaczewski, J.; Eronen, T.; Geldhof, S.; Jokinen, A.; Konieczka, M.; Kostensalo, J.; Moore, I. D.; Nesterenko, D. A.; Penttilä, H.; Pohjalainen, I.; Reponen, M.; Rinta-Antila, S.; de Roubin, A.; Satula, W.; Suhonen, J. (2019)
    An upgraded ion-guide system for the production of neutron-deficient isotopes with heavy-ion beams has been commissioned at the IGISOL facility with an Ar-36 beam on a Ni-nat target. It was used together with the JYFLTRAP double Penning trap to measure the masses of Zr-82, Nb-84, Mo-86, Tc-88, and Ru-89 ground states and the isomeric state Tc-88(m). Of these, Ru-89 and Tc-88(m) weremeasured for the first time. The precision of measurements of Zr-82, Nb-84, and Tc-88 was significantly improved. The literature value for Mo-86 was verified. The measured states in Tc-88 were compared to shell-model calculations and additional constraints on the spins and level scheme were obtained. The masses of Mo-82 and Ru-86 have been predicted using the measured masses of their mirror partners and theoretical mirror displacement energies, resulting in more tightly bound nuclei with smaller atomic mass uncertainties than reported in the literature.
  • Mattinen, Miika; Hatanpaa, Timo; Mizohata, Kenichiro; Raisanen, Jyrki; Leskela, Markku; Ritala, Mikko (2021)
    Co9S8 is an interesting sulfide material with metallic conductivity that has shown promise for various energy applications. Herein, we report a new atomic layer deposition process producing crystalline, pure, and highly conductive Co9S8 thin films using CoCl2(TMEDA) (TMEDA = N,N,N ',N '-tetramethylethylenediamine) and H2S as precursors at 180-300 degrees C. The lowest resistivity of 80 mu omega cm, best uniformity, and highest growth rate are achieved at 275 degrees C. Area-selective deposition is enabled by inherent substrate-dependency of film nucleation. We show that a continuous and conductive Co9S8 film can be prepared on oxide-covered silicon without any growth on Si-H. Besides silicon, Co9S8 films can be grown on a variety of substrates. The first example of an epitaxial Co9S8 film is shown using a GaN substrate. The Co9S8 films are stable up to 750 degrees C in N-2, 400 degrees C in forming gas, and 225 degrees C in O-2 atmosphere. The reported ALD process offers a scalable and cost-effective route to high-quality Co9S8 films, which are of interest for applications ranging from electrocatalysis and rechargeable batteries to metal barrier and liner layers in microelectronics and beyond.
  • Trochowski, Mateusz; Kobielusz, Marcin; Mroz, Krystian; Surowka, Marcin Karol; Hämäläinen, Jani; Iivonen, Tomi; Leskelä, Markku; Macyk, Wojciech (2019)
    Synthetic procedures, including doping, sintering and surface coating, can noticeably affect the physicochemical properties of semiconductors. Introduced changes very often translate into photocatalytic and photoelectrochemical activity alterations. However, in this work we have focused on more subtle treatments, which result in lack of changes observed using XRD, UV-vis, porosimetry, TEM or SEM. We have subjected titanium dioxide (P25, UV100) to a treatment with reducing agents used in procedures of noble metal deposition (citrate, borohydride, and photoreduction), or surface decoration with small amounts of TiO2 by atomic layer deposition (ALD; 10 to 200 deposition cycles), which presumably should be neutral to its activity. Although the "classical" characterization methods did not show any differences between the original and treated samples, spectroelectrochemical (SE-DRS) determination of the density of states (DOS) and catechol adsorption tests revealed a significant influence of such treatments on the photocatalytic activity (photogeneration of HO radicals, water reduction, and herbicide degradation) and photoelectrochemical behaviour of the studied samples. We have shown that the applied slight surface modifications of titanium dioxide ("insignificant" at the first glance) may strongly affect the activity of this material. Such often overlooked effects must be taken into account during a comparative photoactivity analysis of various semiconductors, since an insignificant surface treatment may noticeably influence surface chemistry. We have also demonstrated that SE-DRS can be considered as a useful tool to study these effects, although it can be difficult to correlate a particular treatment with recorded changes in the density of states.
  • Hamedani, A.; Byggmästar, J.; Djurabekova, F.; Alahyarizadeh, G.; Ghaderi, R.; Minuchehr, A.; Nordlund, K. (2020)
    We develop a silicon Gaussian approximation machine learning potential suitable for radiation effects, and use it for the first ab initio simulation of primary damage and evolution of collision cascades. The model reliability is confirmed by good reproduction of experimentally measured threshold displacement energies and sputtering yields. We find that clustering and recrystallization of radiation-induced defects, propagation pattern of cascades, and coordination defects in the heat spike phase show striking differences to the widely used analytical potentials. The results reveal that small defect clusters are predominant and show new defect structures such as a vacancy surrounded by three interstitials. Impact statement Quantum-mechanical level of accuracy in simulation of primary damage was achieved by a silicon machine learning potential. The results show quantitative and qualitative differences from the damage predicted by any previous models.
  • Hyvärinen, Kati; Holopainen, Minna; Skirdenko, Vita; Ruhanen, Hanna; Lehenkari, Petri; Korhonen, Matti; Käkelä, Reijo; Laitinen, Saara; Kerkelä, Erja (2018)
    Resolution-phase macrophage population orchestrates active dampening of the inflammation by secreting anti-inflammatory and proresolving products including interleukin (IL)-10 and lipid mediators (LMs). We investigated the effects of both human bone marrow-derived mesenchymal stromal cells (MSCs) and MSC-derived extracellular vesicles (MSC-EVs) on mature human regulatory macrophages (Mregs). The cytokines and LMs were determined from cell culture media of Mregs cultivated with MSCs and MSC-EVs. In addition, the alterations in the expression of cell surface markers and the phagocytic ability of Mregs were investigated. Our novel findings indicate that both MSC coculture and MSC-EVs downregulated the production of IL-23 and IL-22 enhancing the anti-inflammatory phenotype of Mregs and amplifying proresolving properties. The levels of prostaglandin E-2 (PGE(2)) were substantially upregulated in MSC coculture media, which may endorse proresolving LM class switching. In addition, our results manifest, for the first time, that MSC-EVs mediate the Mreg phenotype change via PGE(2). These data suggest that both human MSC and MSC-EVs may potentiate tolerance-promoting proresolving phenotype of human Mregs.
  • Kudinov, A. A.; Mantysaari, E. A.; Aamand, G. P.; Uimari, P.; Stranden, I. (2020)
  • Wrigstedt, P.; Keskiväli, J.; Repo, T. (2016)
    We describe herein an efficient microwave-assisted aqueous biphasic dehydration of carbohydrates to 5-hydroxymethylfurfural (HMF). The effects of several alkali metal salts in aqueous phase, organic solvents as an extractive phase and Lewis acids are evaluated on the reaction. Specifically, starting from fructose, the use of bromide salts in aqueous phase and the common organic solvent MeCN or lignocellulose-derived gamma-valerolactone (GVL) as organic extractors are highly beneficial, leading to excellent HMF yields of up to 91% with HCl as a Bronsted acid catalyst. In conjunction with an isomerization catalyst, the method was applicable to glucose as well as various disaccharides and cellulose, affording HMF in notably good yields, particularly with GVL as an extractor and reusable Amberlyst-38(wet) as an acid catalyst. The exceptionally high HMF yields obtained in aqueous solutions is attributed to the combined effect of the biphasic reaction system and the application of microwaves, which ensures short reaction times and minimized by-product formation thereof.