654 research outputs found
Transport phenomena and decoherence in short Josephson junction arrays
No full textunknown accessibilityei tietoa saavutettavuudest
upper-polariton/GROMACS-4.5.3-multi_mode_Tavis-Cummings: v1.0.0
No full textCode from https://github.com/rhti/gromacs_qed
In this fork of GROMACS version 4.5.3 we have implemented routines in qm_gaussian.c to perform multi-mode Tavis Cummings QM/MM simulations of molecules in optical cavities.
Papers describing the implementation:
1) Extension of 2-level system in Tavis Cummings model to QM/MM description of molecules, for a single mode cavity:
Multiscale molecular dynamics simulations of polaritonic chemistry
HL Luk, J Feist, JJ Toppari, G Groenhof
Journal of chemical theory and computation 13 (9), 4324-4335
2) Implementation of Fewest-Switches Surface Hopping
Coherent light harvesting through strong coupling to confined light
G Groenhof, JJ Toppari
The journal of physical chemistry letters 9 (17), 4848-4851
3) Implementation of Mean-Field MD
Tracking polariton relaxation with multiscale molecular dynamics simulations
G Groenhof, C Climent, J Feist, D Morozov, JJ Toppari
The journal of physical chemistry letters 10 (18), 5476-5483
4) Implementation of Multipple Cavity Modes, following Michetti and La Rocca in Phys Rev. B 71 (2015) 115320
Multi-scale dynamics simulations of molecular polaritons: The effect of multiple cavity modes on polariton relaxation
RH Tichauer, J Feist, G Groenhof
The Journal of Chemical Physics 154 (10)
The work was funded by the Academy of Finland
installation requires MPI, LAPACK and FFTW libraries
Instructions for setting up a system and in share/examples.mmT
First Infant Formula Type and Risk of Islet Autoimmunity
No full textSAS and R code for the statistical analysis of the following publication:
Hummel S, Beyerlein A, Tamura R, Uusitalo U, Andrén Aronsson C, Yang J, Riikonen A, Lernmark Å, Rewers MJ, Hagopian WA, She JX, Simell OG, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Virtanen SM, Norris JM; TEDDY Study Group: First Infant Formula Type and Risk of Islet Autoimmunity in The Environmental Determinants of Diabetes in the Young (TEDDY) Study. Diabetes Care 2017; 40(3):398-40
Progression from islet autoimmunity to clinical type 1 diabetes is influenced by genetic factors
No full textR code for the statistical analysis of the following publication:
Beyerlein A, Bonifacio E, Vehik K, Hippich M, Winkler C, Frohnert BI, Steck AK, Hagopian WA, Krischer JP, Lernmark Å, Rewers MJ, She JX, Toppari J, Akolkar B, Rich SS, Ziegler AG; TEDDY Study Group: Progression from islet autoimmunity to clinical type 1 diabetes is influenced by genetic factors: results from the prospective TEDDY study. J Med Genet. 2019; 56(9):602-60
Genetic scores to stratify risk of developing multiple islet autoantibodies and type 1 diabetes.
No full textR code for the statistical analysis of the following publication:
Bonifacio E, Beyerlein A, Hippich M, Winkler C, Vehik K, Weedon MN, Laimighofer M, Hattersley AT, Krumsiek J, Frohnert BI, Steck AK, Hagopian WA, Krischer JP, Lernmark Å, Rewers MJ, She JX, Toppari J, Akolkar B, Oram RA, Rich SS, Ziegler AG; TEDDY Study Group: Genetic scores to stratify risk of developing multiple islet autoantibodies and type 1 diabetes: A prospective study in children. PLoS Med. 2018; 15(4):e100254
Fetal but not adult Leydig cells are susceptible to adenoma formation in response to persistently high hCG level; a study on hCG overexpressing transgenic mice
No full textWe have previously demonstrated that male transgenic (TG) mice overexpressing human chorionic gonadotropin (hCG+) develop reproductive organ defects, but no tumors, in adult age. In this study, the effects of persistently elevated hCG were followed in TG males between day 5 postpartum and adulthood. Leydig cell (LC) adenomas were found in prepubertal mice, most prominently at the age of 10 days, but not in adult age. Serum testosterone concentrations were significantly increased in TG males at all ages studied. The phenotype of the prepubertal hCG+ males resembled that found in boys upon expression of constitutively activating luteinizing hormone (LH) receptor mutations. The temporal expression patterns of the fetal LC marker gene, thrombospondin 2, and those of adult LCs, hydroxysteroid dehydrogenase-6, delta5-3-beta and prostaglandin D synthase, were similar in wild-type and hCG+ males. Hence, the postnatal adenomas resemble functionally fetal LCs, and only these cells are susceptible to hCG-induced tumorigenesis. Our findings demonstrate a novel intriguing difference between the fetal and adult LC populations and provide further insight into the potential tumorigenic effects of gonadotropins.Fil: Ahtianen, Petteri. University of Turku; FinlandiaFil: Rulli, Susana Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Shariatmadari, Ramin. University of Turku; FinlandiaFil: Pelliniemi, Lauri J.. University of Turku; FinlandiaFil: Toppari, Jorma. University of Turku; FinlandiaFil: Poutanen, Matti. University of Turku; FinlandiaFil: Huhtaniemi, Ilpo T.. University of Turku; Finlandia. Imperial College London; Reino Unid
Antiviral action of a functionalized plastic surface against human coronaviruses
No full textViruses may persist on solid surfaces for long periods, which may contribute to indirect transmission. Thus, it is imperative to develop functionalized surfaces that will lower the infectious viral load in everyday life. Here, we have tested a plastic surface functionalized with tall oil rosin against the seasonal human coronavirus OC43 as well as severe acute respiratory syndrome coronavirus 2. All tested non-functionalized plastic surfaces showed virus persistence up to 48 h. In contrast, the functionalized plastic showed good antiviral action already within 15 min of contact and excellent efficacy after 30 min over 90% humidity. Excellent antiviral effects were also observed at lower humidities of 20% and 40%. Despite the hydrophilic nature of the functionalized plastic, viruses did not adhere strongly to it. According to helium ion microscopy, viruses appeared flatter on the rosin-functionalized surface, but after flushing away from the rosin-functionalized surface, they showed no apparent structural changes when imaged by transmission electron microscopy of cryogenic or negatively stained specimens or by atomic force microscopy. Flushed viruses were able to bind to their host cell surface and enter endosomes, suggesting that the fusion with the endosomal membrane was halted. The eluted rosin from the functionalized surface demonstrated its ability to inactivate viruses, indicating that the antiviral efficacy relied on the active leaching of the antiviral substances, which acted on the viruses coming into contact. The rosin-functionalized plastic thus serves as a promising candidate as an antiviral surface for enveloped viruses.peerReviewe
GnRH antagonist treatment of malignant adrenocortical tumors
No full textAberrantly expressed G protein-coupled receptors in tumors are considered as potential therapeutic targets. We analyzed the expressions of receptors of gonadotropin-releasing hormone (GNRHR), luteinizing hormone/chorionic gonadotropin (LHCGR) and follicle-stimulating hormone (FSHR) in human adrenocortical carcinomas and assessed their response to GnRH antagonist therapy. We further studied the effects of the GnRH antagonist cetrorelix acetate (CTX) on cultured adrenocortical tumor (ACT) cells (mouse C alpha 1 and Y-1, and human H295R), and in vivo in transgenic mice (SV40 T-antigen expression under inhibin a promoter) bearing Lhcgr and Gnrhr in ACT. Both models were treated with control (CT), CTX, human chorionic gonadotropin (hCG) or CTX+hCG, and their growth and transcriptional changes were analyzed. In situ hybridization and qPCR analysis of human adrenocortical carcinomas (n = 11-13) showed expression of GNRHR in 54/73%, LHCGR in 77/100% and FSHR in 0%, respectively. CTX treatment in vitro decreased cell viability and proliferation, and increased caspase 3/7 activity in all treated cells. In vivo, CTX and CTX+hCG (but not hCG alone) decreased ACT weights and serum LH and progesterone concentrations. CTX treatment downregulated the tumor markers Lhcgr and Gata4. Upregulated genes included Grb10, Rerg, Nfatc and Gnas, all recently found to be abundantly expressed in healthy adrenal vs ACT. Our data suggest that CTX treatment may improve the therapy of human adrenocortical carcinomas by direct action on GNRHR-positive cancer cells inducing apoptosis and/or reducing gonadotropin release, directing tumor cells towards a healthy adrenal gene expression profile
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