Browsing by Subject "PROBE"

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  • Kiiveri, K.; Gruen, D.; Finoguenov, A.; Erben, T.; van Waerbeke, L.; Rykoff, E.; Miller, L.; Hagstotz, S.; Dupke, R.; Henry, J. Patrick; Kneib, J-P; Gozaliasl, G.; Kirkpatrick , C. C.; Cibirka, N.; Clerc, N.; Costanzi, M.; Cypriano, E. S.; Rozo, E.; Shan, H.; Spinelli, P.; Valiviita, J.; Weller, J. (2021)
    The COnstrain Dark Energy with X-ray clusters (CODEX) sample contains the largest flux limited sample of X-ray clusters at 0.35 <z <0.65. It was selected from ROSAT data in the 10 000 square degrees of overlap with BOSS, mapping a total number of 2770 high-z galaxy clusters. We present here the full results of the CFHT CODEX programme on cluster mass measurement, including a reanalysis of CFHTLS Wide data, with 25 individual lensing-constrained cluster masses. We employ LENSFIT shape measurement and perform a conservative colour-space selection and weighting of background galaxies. Using the combination of shape noise and an analytic covariance for intrinsic variations of cluster profiles at fixed mass due to large-scale structure, miscentring, and variations in concentration and ellipticity, we determine the likelihood of the observed shear signal as a function of true mass for each cluster. We combine 25 individual cluster mass likelihoods in a Bayesian hierarchical scheme with the inclusion of optical and X-ray selection functions to derive constraints on the slope alpha, normalization beta, and scatter sigma(ln lambda vertical bar mu) of our richness-mass scaling relation model in log-space: <In lambda vertical bar mu > = alpha mu + beta, with mu = ln (M-200c/M-piv), and M-piv = 10(14.81)M(circle dot). We find a slope alpha = 0.49(-0.15)(+0.20) , normalization exp(beta) = 84.0(-14.8)(+9.2) , and sigma(ln lambda vertical bar mu) = 0.17(-0.09)(+0.13) using CFHT richness estimates. In comparison to other weak lensing richness-mass relations, we find the normalization of the richness statistically agreeing with the normalization of other scaling relations from a broad redshift range (0.0 <z <0.65) and with different cluster selection (X-ray, Sunyaev-Zeldovich, and optical).
  • Fedorowicz, Joanna; Bazar, Dagmara; Brankiewicz, Wioletta; Kapica, Hanna; Ciura, Krzesimir; Zalewska-Piatek, Beata; Piatek, Rafal; Cal, Krzysztof; Mojsiewicz-Pienkowska, Krystyna; Saczewski, Jaroslaw (2022)
    Low-molecular synthetic fluorophores are convenient tools in bioimaging applications. Several derivatives of Safirinium dyes as well as their reactive N-hydroxysuccinimide (NHS) esters bearing diverse substituents were synthesized and evaluated experimentally in terms of their lipophilicity by means of reverse-phase and immobilized artificial membrane high-performance liquid chromatography. Subsequently, the selected compounds were employed as novel cellular imaging agents for staining Gram-positive and Gram-negative bacteria, human kidney cell line, as well as human skin tissue. The analyzed dyes allowed for visualization of cellular structures such as mitochondria, endoplasmic reticulum, and cellular nuclei. They proved to be useful in fluorescent staining of stratum corneum, especially in the aspect of xenobiotic exposure and its penetration into the skin. The best results were obtained with the use of moderately lipophilic NHS esters of Safirinium Q. The development of Safirinium dyes is a promising alternative for commercially available dyes since the reported molecules have low molecular masses and exhibit efficient staining and remarkable water solubility. Moreover, they are relatively simple and low-cost in synthesis.
  • The CMS collaboration; Sirunyan, A. M.; Eerola, P.; Forthomme, L.; Kirschenmann, H.; Österberg, K.; Voutilainen, M.; Garcia, F.; Havukainen, J.; Heikkilä, J. K.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampen, T.; Lassila-Perini, K.; Laurila, S.; Lehti, S.; Linden, T.; Luukka, P.; Mäenpää, T.; Siikonen, H.; Tuominen, E.; Tuominiemi, J.; Tuuva, T.; Pekkanen, J.; Tumasyan, A. (2020)
    A search forWWproduction from double-parton scattering processes using same-charge electron-muon and dimuon events is reported, based on proton-proton collision data collected at a center-of-mass energy of 13 TeV. The analyzed data set corresponds to an integrated luminosity of 77.4 fb-1, collected using the CMS detector at the LHC in 2016 and 2017. Multivariate classifiers are used to discriminate between the signal and the dominant background processes. A maximum likelihood fit is performed to extract the signal cross section. This leads to the first evidence for WW production via double-parton scattering, with a significance of 3.9 standard deviations. The measured inclusive cross section is 1.41 +/- 0.28 (stat) +/- 0.28 (syst) pb.
  • Ducloué, B.; Szymanowski, L.; Wallon, S. (2016)
    We study the production of two forward jets with a large interval of rapidity at hadron colliders, which was proposed by Mueller and Navelet as a possible test of the high energy dynamics of QCD, within a complete next-to-leading logarithm framework. We show that using the Brodsky-Lepage-Mackenzie procedure to fix the renormalization scale leads to a very good description of the recent CMS data at the LHC for the azimuthal correlations of the jets. We show that the inclusion of next-to-leading order corrections to the jet vertex significantly reduces the importance of energy-momentum non-conservation which is inherent to the BFKL approach, for an asymmetric jet configuration. Finally, we argue that the double parton scattering contribution is negligible in the kinematics of actual CMS measurements.
  • Song, Yun-Qing; Weng, Zi-Miao; Dou, Tong-Yi; Finel, Moshe; Wang, Ya-Qiao; Ding, Le-Le; Jin, Qiang; Wang, Dan-Dan; Fang, Sheng-Quan; Cao, Yun-Feng; Hou, Jie; Ge, Guang-Bo (2019)
    Magnolol, the most abundant bioactive constituent of the Chinese herb Magnolia officinalis, has been found with multiple biological activities, including anti-oxidative, anti-inflammatory and enzyme-regulatory activities. In this study, the inhibitory effects and inhibition mechanism of magnolol on human carboxylesterases (hCEs), the key enzymes responsible for the hydrolytic metabolism of a variety of endogenous esters as well as ester-bearing drugs, have been well-investigated. The results demonstrate that magnolol strongly inhibits hCE1-mediated hydrolysis of various substrates, whereas the inhibition of hCE2 by magnolol is substrate-dependent, ranging from strong to moderate. Inhibition of intracellular hCE1 and hCE2 by magnolol was also investigated in living HepG2 cells, and the results showed that magnolol could strongly inhibit intracellular hCE1, while the inhibition of intracellular hCE2 was weak. Inhibition kinetic analyses and docking simulations revealed that magnolol inhibited both hCE1 and hCE2 in a mixed manner, which could be partially attributed to its binding at two distinct ligand-binding sites in each carboxylesterase, including the catalytic cavity and the regulatory domain. In addition, the potential risk of the metabolic interactions of magnolol via hCE1 inhibition was predicted on the basis of a series of available pharmacokinetic data and the inhibition constants. All these findings are very helpful in deciphering the metabolic interactions between magnolol and hCEs, and also very useful for avoiding deleterious interactions via inhibition of hCEs.
  • Hynönen, Ulla; Zoetendal, Erwin G.; Virtala, Anna-Maija K.; Shetty, Sudarshan; Hasan, Shah; Jakava-Viljanen, Miia; de Vos, Willem M.; Palva, Airi (2020)
    In our previous studies on irritable bowel syndrome (IBS) –associated microbiota by molecular methods, we demonstrated that a particular 16S rRNA gene amplicon was more abundant in the feces of healthy subjects or mixed type IBS (IBS-M) –sufferers than in the feces of individuals with diarrhea-type IBS (IBS-D). In the current study, we demonstrated that this, so called Ct85-amplicon, consists of a cluster of very heterogeneous 16S rRNA gene sequences, and defined six 16S rRNA gene types, a to f, within this cluster, each representing a novel species-, genus- or family level taxon. We then designed specific PCR primers for these sequence types, mapped the distribution of the Ct85-cluster sequences and that of the newly defined sequence types in several animal species and compared the sequence types present in the feces of healthy individuals and IBS sufferers using two IBS study cohorts, Finnish and Dutch. Various Ct85-cluster sequence types were detected in the fecal samples of several companion and production animal species with remarkably differing prevalences and abundances. The Ct85 sequence type composition of swine closely resembled that of humans. One of the five types (d) shared between humans and swine was not present in any other animals tested, while one sequence type (b) was found only in human samples. In both IBS study cohorts, one type (e) was more prevalent in healthy individuals than in the IBS-M group. By revealing various sequence types in the widespread Ct85-cluster and their distribution, the results improve our understanding of these uncultured bacteria, which is essential for future efforts to cultivate representatives of the Ct85-cluster and reveal their roles in IBS.
  • Kalendar, Ruslan; Shustov, Alexandr; Seppänen, Mervi Mirjam; Schulman, Alan Howard; Stoddard, Frederick Lothrop (2019)
    Genome walking (GW) refers to the capture and sequencing of unknown regions in a long DNA molecule that are adjacent to a region with a known sequence. A novel PCR-based method, palindromic sequence-targeted PCR (PST-PCR), was developed. PST-PCR is based on a distinctive design of walking primers and special thermal cycling conditions. The walking primers (PST primers) match palindromic sequences (PST sites) that are randomly distributed in natural DNA. The PST primers have palindromic sequences at their 3’ ends. Upstream of the palindromes there is a degenerate sequence (8-12 nucleotides long); defined adapters are present at the 5’-termini. The thermal cycling profile has a linear amplification phase and an exponential amplification phase differing in annealing temperature. Changing the annealing temperature to switch the amplification phases at a defined cycle controls the balance between sensitivity and specificity. In contrast to traditional genome walking methods, PST-PCR is rapid (two to three hours to produce GW fragments) as it uses only one or two PCR rounds. Using PST-PCR, previously unknown regions (the promoter and intron 1) of the VRN1 gene of Timothy-grass (Phleum pratense L.) were captured for sequencing. In our experience, PST-PCR had higher throughput and greater convenience in comparison to other GW methods.
  • Zakharov, Danila O.; Chernichenko, Konstantin; Sorochkina, Kristina; Yang, Shengjun; Telkki, Ville-Veikko; Repo, Timo; Zhivonitko, Vladimir V. (2022)
    We report nuclear spin hyperpolarization of various alkenes achieved in alkyne hydrogenations with parahydrogen over a metal-free hydroborane catalyst (HCAT). Being an intramolecular frustrated Lewis pair aminoborane, HCAT utilizes a non-pairwise mechanism of H-2 transfer to alkynes that normally prevents parahydrogen-induced polarization (PHIP) from being observed. Nevertheless, the specific spin dynamics in catalytic intermediates leads to the hyperpolarization of predominantly one hydrogen in alkene. PHIP enabled the detection of important HCAT-alkyne-H-2 intermediates through substantial H-1, B-11 and N-15 signal enhancement and allowed advanced characterization of the catalytic process.
  • Zakharov, Danila O.; Chernichenko, Konstantin; Sorochkina, Kristina; Repo, Timo; Zhivonitko, Vladimir V. (2022)
    Parahydrogen-induced polarization is a nuclear spin hyperpolarization technique that can provide strongly enhanced NMR signals for catalytic hydrogenation reaction products and intermediates. Among other matters, this can be employed to study the mechanisms of the corresponding chemical transformations. Commonly, noble metal complexes are used for reactions with parahydrogen. Herein, we present a PHIP study of metal-free imine hydrogenations catalyzed by the ansa-aminoborane catalyst QCAT. We discuss the reaction mechanism by showing the pairwise nature of the initial hydrogen activation step that leads to the formation of the negative net nuclear spin polarization of N-H hydrogen in the QCAT-H-2 intermediate, enabling the further transfer of parahydrogen-originating protons to the imine substrate with the accumulation of hyperpolarized amine products. Parahydrogen-induced polarization also demonstrates the reversibility of the catalytic cycle.
  • The ALICE collaboration; Acharya, S.; Adamova, D.; Kim, D. J.; Krizek, F.; Parkkila, J. E.; Rak, J.; Rytkönen, Heidi Maria; Räsänen, Sami; Saarimäki, Oskari Antti Matti; Slupecki, M.; Trzaska, W. H.; Zhou, Zhipeng (2021)
    In this paper, the first femtoscopic analysis of pion-kaon correlations at the LHC is reported. The analysis was performed on the Pb-Pb collision data at root(S)(NN) = 2.76 TeV recorded with the ALICE detector. The non-identical particle correlations probe the spatio-temporal separation between sources of different particle species as well as the average source size of the emitting system. The sizes of the pion and kaon sources increase with centrality, and pions are emitted closer to the centre of the system and/or later than kaons. This is naturally expected in a system with strong radial flow and is qualitatively reproduced by hydrodynamic models. ALICE data on pion-kaon emission asymmetry are consistent with (3+1)-dimensional viscous hydrodynamics coupled to a statistical hadronisation model, resonance propagation, and decay code THERMINATOR 2 calculation, with an additional time delay between 1 and 2 fm/c for kaons. The delay can be interpreted as evidence for a significant hadronic rescattering phase in heavy-ion collisions at the LHC. (C) 2020 The Author. Published by Elsevier B.V.