| 41. |
- Abel, Frida, 1974, et al.
(författare)
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Mutations in the N-terminal domain of DFF45 in a primary germ cell tumor and in neuroblastoma tumors.
- 2004
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Ingår i: International journal of oncology. - 1019-6439 .- 1791-2423. ; 25:5, s. 1297-302
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Tidskriftsartikel (refereegranskat)abstract
- DFF45 has essential functions in the final stage of apoptosis by acting both as a folding chaperone and a DNase inhibitor of DFF40. The gene encoding DFF45 (DFFA) maps to the consensus deleted region in primary neuroblastoma (NB; 1p36.2-3) and within the homozygously deleted region in an NB cell line (1p36.2). DFF45 is therefore an attractive candidate NB tumor suppressor. In a previous study we found a rare allele variant, causing a non-polar to a polar amino acid exchange (Ile69Thr) in a preserved hydrophobic patch of DFF45, and we also found DFFA to be preferentially expressed in favorable NB tumors. We have extended the previous study and performed mutation analyses in another 56 NB tumors (100 in total) as well as a set of other tumors for coding mutations in DFFA. We have also performed studies of the DFFA expression in tumors using real-time PCR. We found a missense mutation (Ile15Met) in the remaining allele of a teratoma with heterozygous deletion of 1p, and a three base-pair deletion in an NB of unknown stage causing a deletion of amino acid 37 in DFF45. The one-base substitution detected in the teratoma was not present in the patients constitutional DNA, i.e. it is a true mutation present in the tumor DNA only. In conclusion, three different coding alterations have been found in the region encoding the N-terminal regulatory domain of DFF45, responsible for binding and achieving its chaperone and inhibitor functions on other proteins. Moreover, by real-time RT-PCR expression study, we found the mRNA level of DFFA to be significantly (p=0.038) reduced by a factor of 1.7 times in NB tumors of unfavorable outcome.
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| 42. |
- Abenius, Tobias, 1979, et al.
(författare)
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System-scale network modeling of cancer using EPoC
- 2012
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Ingår i: Advances in Experimental Medicine and Biology. - New York, NY : Springer New York. - 0065-2598. - 9781441972095 ; 736:5, s. 617-643
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Tidskriftsartikel (refereegranskat)abstract
- One of the central problems of cancer systems biology is to understand the complex molecular changes of cancerous cells and tissues, and use this understanding to support the development of new targeted therapies. EPoC (Endogenous Perturbation analysis of Cancer) is a network modeling technique for tumor molecular profiles. EPoC models are constructed from combined copy number aberration (CNA) and mRNA data and aim to (1) identify genes whose copy number aberrations significantly affect target mRNA expression and (2) generate markers for long- and short-term survival of cancer patients. Models are constructed by a combination of regression and bootstrapping methods. Prognostic scores are obtained from a singular value decomposition of the networks. We have previously analyzed the performance of EPoC using glioblastoma data from The Cancer Genome Atlas (TCGA) consortium, and have shown that resulting network models contain both known and candidate disease-relevant genes as network hubs, as well as uncover predictors of patient survival. Here, we give a practical guide how to perform EPoC modeling in practice using R, and present a set of alternative modeling frameworks.
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| 43. |
- Aberšek, Nina, et al.
(författare)
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Calprotectin levels in amniotic fluid in relation to intra-amniotic inflammation and infection in women with preterm labor with intact membranes: A retrospective cohort study
- 2022
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Ingår i: European Journal of Obstetrics & Gynecology and Reproductive Biology. - : Elsevier BV. - 1872-7654 .- 0301-2115. ; 272, s. 24-29
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To evaluate the concentrations of calprotectin in amniotic fluid with respect to intra-amniotic inflammation and infection and to assess the presence or absence of bacteria in the amnio-chorionic niche with respect to presence or absence of intra-amniotic inflammation. Study design: Seventy-nine women with singleton pregnancies and preterm labor with intact membranes (PTL) were included in the study. Amniotic fluid was collected at the time of admission by amniocentesis and calprotectin levels were analyzed from frozen/thawed samples using ELISA. Interleukin (IL)-6 concentration was measured by point-of-care test. Samples from amniotic fluid and the amnio-chorionic niche (space between amniotic and chorionic membranes) were microbiologically analyzed. Microbial invasion of the amniotic cavity (MIAC) was diagnosed based on a positive PCR result for Ureaplasma species, Mycoplasma hominis, 16S rRNA or positive culture. Intra-amniotic inflammation (IAI) was defined as amniotic fluid point-of-care IL-6 concentration ≥ 745 pg/mL. The cohort of included women was divided into 4 subgroups based on the presence or absence of IAI/MIAC; i) intra-amniotic infection, ii) sterile IAI, iii) intra-amniotic colonization and iv) neither MIAC nor IAI. Results: Women with intra-amniotic infection had a significantly higher intra-amniotic calprotectin concentration (median; 101.6 µg/mL) compared with women with sterile IAI (median; 9.2 µg/mL), women with intra-amniotic colonization (median; 2.6 µg/mL) and women with neither MIAC nor IAI (median 4.6 µg/mL) (p = 0.001). Moreover, significantly higher amniotic fluid calprotectin concentration was seen in women who delivered within 7 days (p = 0.003). A significant negative correlation was found between amniotic fluid calprotectin and gestational age at delivery (rho = 0.32, p = 0.003). Relatively more bacteria in the amnio-chorionic niche were found in the sterile IAI group compared with the other groups. Conclusions: Calprotectin concentrations in amniotic fluid were significantly higher in the intra-amniotic infection group compared with the other groups. Moreover, the bacterial presence in the amnio-chorionic niche was higher in IAI group.
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| 44. |
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| 45. |
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| 46. |
- Abrahamsson, Christoffer, 1984, et al.
(författare)
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Magnetically induced structural anisotropy in binary colloidal gels and its effect on diffusion and pressure driven permeability
- 2014
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Ingår i: Soft Matter. - 1744-683X .- 1744-6848. ; 10:24, s. 4403-4412
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Tidskriftsartikel (refereegranskat)abstract
- We report on the synthesis, microstructure and mass transport properties of a colloidal hydrogel selfassembled from a mixture of colloidal silica and nontronite clay plates at different particle concentrations. The gel-structure had uniaxial long-range anisotropy caused by alignment of the clay particles in a strong external magnetic field. After gelation the colloidal silica covered the clay particle network, fixing the orientation of the clay plates. Comparing gels with a clay concentration between 0 and 0.7 vol%, the magnetically oriented gels had a maximum water permeability and self-diffusion coefficient at 0.3 and 0.7 vol% clay, respectively. Hence the specific clay concentration resulting in the highest liquid flux was pressure dependent. This study gives new insight into the effect of anisotropy, particle concentration and bound water on mass transport properties in nano/microporous materials. Such findings merit consideration when designing porous composite materials for use in for example fuel cell, chromatography and membrane technology.
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| 47. |
- Abrahamsson, Erik, 1974, et al.
(författare)
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A new reaction path for the C + NO reaction: dynamics on the 4A'' potential-energy surface.
- 2008
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Ingår i: Physical chemistry chemical physics : PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 10:30, s. 4400-9
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Tidskriftsartikel (refereegranskat)abstract
- We present a new reaction path without significant barriers for the C + NO reaction, forming ground state N((4)S) and CO. Electronic structure (CASPT2) calculations have been performed for the two lowest (4)A'' states of the CNO system. The lowest of these states shows no significant barriers against reaction in the C + NO or O + CN channels. This surface has been fitted to an analytical function using a many-body expansion. Using this surface, and the previously published (2)A' and (2)A'' surfaces [Andersson et al., Phys. Chem. Chem. Phys., 2000, 2, 613; Andersson et al., Chem. Phys., 2000, 259, 99], we have performed quasiclassical trajectory (QCT) calculations, obtaining rate coefficients for the C((3)P) + NO(X(2)Pi) --> CO(X(1)Sigma(+)) + N((4)S,(2)D) and C((3)P) + NO(X(2)Pi) --> O((3)P) + CN(X(2)Sigma(+)) reactions. We have also simulated the crossed molecular beam experiments of Naulin et al. [Chem. Phys., 1991, 153, 519] The inclusion of the (4)A'' surface in the QCT calculations gives excellent agreement with experiments. This is the first time an adiabatic pathway from C((3)P) + NO(X(2)Pi) to CO(X(1)Sigma(+))+N((4)S) has been reported.
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| 48. |
- Abrahamsson, Erik, 1974, et al.
(författare)
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Classical and quantum dynamics of the O+CN reaction
- 2006
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Ingår i: Chemical Physics. - : Elsevier BV. - 0301-0104. ; 324:2-3, s. 507-514
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Tidskriftsartikel (refereegranskat)abstract
- Electronic structure (CASPT2) calculations have been performed for the (2)Pi and (4)Sigma(-) states of the NCO system. To create the potential energy surfaces, the generalized discrete variable representation (GDVR) method has been used. Wave packet calculations have been performed for the collinear O + CN reaction on both surfaces. These are the first reported quantum dynamics calculations on this reaction. State-to-state reaction probabilities are presented. On the (2)Pi surface, which has an almost 6 eV deep well, we obtain structure in the reaction probabilities at low kinetic energies but at higher energies they are smooth. The (4)Sigma(-) surface is highly exoergic and vibrationally non-adiabatic dynamics is observed. The (4)Sigma(-) surface has an early barrier and as a result we find that translational energy more efficiently promotes the reaction than vibrational energy does. The wave packet results are compared with QCT results. Generally the agreement is good as would be expected but some notable differences are found, particularly for reaction out of the vibrational ground state. (c) 2005 Elsevier B.V. All rights reserved.
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| 49. |
- Abrahamsson, Erik, 1974, et al.
(författare)
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Dynamics of the O + CN Reaction and N + CO Scattering on Two Coupled Surfaces
- 2009
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Ingår i: J. Phys. Chem. A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 113:52, s. 14824-14830
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Tidskriftsartikel (refereegranskat)abstract
- Spin−orbit coupling between the two collinear 2Π and 4Σ− potential energy surfaces for the NCO system are calculated using the RASSI method with CASSCF wave functions as basis set. The GDVR method has been used to interpolate a spin−orbit coupling surface. Wave packet and quasi-classical trajectory surface hopping calculations have been performed and compared for both the O(3P) + CN(X2Σ+) → N(4S) + CO(X1Σ+) reaction and for electronically inelastic scattering in the N + CO channels. The O + CN nonadiabatic reaction probabilities are small. The wavepacket study gives a resonance structure. Also for the N + CO electronically inelastic scattering the wave packet calculations give a distinct resonance structure with peak transition probabilities up to around 10%, which is somewhat lower than the trajectory surface hopping results.
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| 50. |
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