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58 Research products, page 1 of 6

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  • Open Access
    Authors: 
    Fojt, Jakub; Rossi, Tuomas; Kuisma, Mikael; Erhart, Paul;
    Publisher: Zenodo
    Project: EC | RealNanoPlasmon (838996), AKA | Plasmonic nanocatalysts f... (332429)

    This upload includes the codes and input scripts for reproducing the analysis presented in the article "Hot-carrier transfer across a nanoparticle-molecule junction: The importance of orbital hybridization and level alignment" by Jakub Fojt, Tuomas P. Rossi, Mikael Kuisma, and Paul Erhart. The codes reproduce the data of the article provided at doi:10.5281/zenodo.6524101 See README.md in the upload for a detailed description.

  • Open Access English
    Authors: 
    Miyanishi, Yuta;
    Publisher: Zenodo
    Project: EC | ImmerSAFE (764951), AKA | Modeling and Visualizatio... (325530)

    This Simulator computes retinal point spread functions (PSFs) that are rendered by a light field display with varying depths of a rendered point and accommodation distances. For theoretical background, analytical expressions and (most importantly) assumptions and limitations, refer to our paper (Yuta Miyanishi, Erdem Sahin, and Atanas Gotchev. 2022. “Optical Modelling of Accommodative Light Field Display System and Prediction of Human Eye Responses.” Optics Express 30 (21). https://doi.org/10.1364/oe.458651.)

  • Open Access
    Authors: 
    Weir, David James;
    Publisher: Zenodo
    Project: EC | InvisiblesPlus (690575), EC | ELUSIVES (674896), UKRI | Gravitational wave cosmol... (ST/R003904/1), AKA | Particle cosmology and gr... (320123), AKA | BSM physics and primordia... (308791), UKRI | South-Eastern Particle Th... (ST/P000819/1), AKA | Searching for phase trans... (286769), AKA | LISA and the electroweak ... (324882), AKA | Particle cosmology and gr... (319066), NSF | Exploring the Scalar Sect... (1719642),...

    PTPlot is a tool for exploring the gravitational wave power spectrum from first-order phase transitions, and evaluating the likelihood of detecting a signal with the LISA mission. The results plotted by this tool are based on the paper Detecting gravitational waves from cosmological phase transitions with LISA: an update, arXiv:1910.13125, which has been published in JCAP. Please cite both that paper, and this Zenodo deposit, if possible. The source for PTPlot is available at https://bitbucket.org/dweir/ptplot.

  • Research software . 2021
    C++
    Authors: 
    Häkkinen, Antti; Hautaniemi, Sampsa;
    Publisher: bio.tools
    Project: EC | HERCULES (667403), AKA | Efficient computational m... (322927), AKA | Individual variation in r... (314395), AKA | Computational methods to ... (325956), AKA | Personalized combination ... (292402)

    PRISM (Poisson RNA-profile Identification in Scaled Mixtures) is statistical framework that allows simultaneous extraction of a tumor sample composition and cell type and sample specific whole-transcriptome profiles from individual bulk RNA-seq samples, by exploiting single-cell reference data. This facilitates a separate analysis of cancer cell and the microenvironment phenotypes and of the tumor composition.

  • Open Access
    Authors: 
    Häkkinen, Antti; Holmström, Susanna;
    Publisher: Zenodo
    Project: EC | HERCULES (667403), AKA | Efficient computational m... (322927), EC | RESCUER (614154), EC | DECIDER (965193), EC | RESCUER (847912), EC | HERCULES (667403), AKA | Efficient computational m... (322927), EC | RESCUER (614154), EC | DECIDER (965193), EC | RESCUER (847912)

    POIBM is a batch factor inference and correction method that is suited for heterogeneous RNA-seq or other count data datasets. It operates by simulataneously inferring the batch factors and a mapping between matching samples. This is advantageous for datasets, which comprise of samples of heterogeneous populations, in which unknown subpopulations match but e.g. the subpopulation fractions vary so the global population statistics cannot be matched. Major features: Simulatenous batch factor and sample matching inference reveals both the batch correction coefficients and putatively similar phenotypes in the data. The phenotypes need not to be prelabeled, but are learned in the process, as this is often difficult in patient derived samples. Supports sample trimming for datasets that have only very little overlap The model accounts for the discrete nature of RNA-seq data and models both expression and technical noise or the lack of thereof, operates on raw count data, and infers total RNA factors in the process For the details about the method and validation on cancer cell line and patient data, please refer to our publication on the matter.

  • Open Access English
    Authors: 
    Lampilahti, Janne; Manninen, Hanna Elina; Leino, Katri; Väänänen, Riikka; Manninen, Antti; Buenrostro Mazon, Stephany; Nieminen, Tuomo; Leskinen, Matti; Enroth, Joonas; Bister, Marja; +6 more
    Project: EC | ATM-GTP (742206), AKA | ‘Centre of Excellence in ... (272041), AKA | Mechanisms, pathways and ... (314798), AKA | Mechanisms, pathways and ... (314799), EC | ACTRIS-2 (654109), EC | PEGASOS (265148)

    Recent studies have shown the importance of new particle formation (NPF) to global cloud condensation nuclei (CCN) production, as well as to air pollution in megacities. In addition to the necessary presence of low-volatility vapors that can form new aerosol particles, both numerical and observational studies have shown that the dynamics of the planetary boundary layer (BL) plays an important role in NPF. Evidence from field observations suggests that roll vortices might be favorable for inducing NPF in a convective BL. However, direct observations and estimates of the potential importance of this phenomenon to the production of new aerosol particles are lacking. Here we show that rolls frequently induce NPF bursts along the horizontal circulations and that the small clusters and particles originating from these localized bursts grow in size similar to particles typically ascribed to atmospheric NPF that occur almost homogeneously at a regional scale. We outline a method to identify roll-induced NPF from measurements and, based on the collected data, estimate the impact of roll vortices on the overall aerosol particle production due to NPF at a boreal forest site (83 % ± 34 % and 26 % ± 8 % overall enhancement in particle formation for 3 and 10 nm particles, respectively). We conclude that the formation of roll vortices should be taken into account when estimating particle number budgets in the atmospheric BL.

  • Open Access
    Authors: 
    Lubna Dada;
    Publisher: Zenodo
    Project: EC | ACTRIS-2 (654109), EC | ACTRIS PPP (739530), AKA | Centre of Excellence in A... (307331), EC | EMME-CARE (763699), EC | EMME-CARE (856612), EC | ATM-GTP (742206), EC | GASPARCON (714621), AKA | Towards cleaner air: Unde... (316114), EC | CHAPAs (850614), AKA | Molecular steps of gas-to... (296628),...

    A plug-and-play MATLAB code used to calculate the sulfuric acid proxy concentration at any location around the world given that the precursor concentrations are available (SO2, global radiation, condensation sink, O3, alkenes) and the concentration of these precursors lies within the range of precursors measured at one of the locations studied in Dada et al. (2020). Cite also: Dada, L., Ylivinkka, I., Baalbaki, R., Li, C., Guo, Y., Yan, C., Yao, L., Sarnela, N., Jokinen, T., Daellenbach, K. R., Yin, R., Deng, C., Chu, B., Nieminen, T., Wang, Y., Lin, Z., Thakur, R. C., Kontkanen, J., Stolzenburg, D., Sipilä, M., Hussein, T., Paasonen, P., Bianchi, F., Salma, I., Weidinger, T., Pikridas, M., Sciare, J., Jiang, J., Liu, Y., Petäjä, T., Kerminen, V.-M., and Kulmala, M.: Sources and sinks driving sulfuric acid concentrations in contrasting environments: implications on proxy calculations, Atmos. Chem. Phys., 20, 11747–11766, https://doi.org/10.5194/acp-20-11747-2020, 2020. {"references": ["Dada, L., Ylivinkka, I., Baalbaki, R., Li, C., Guo, Y., Yan, C., Yao, L., Sarnela, N., Jokinen, T., Daellenbach, K. R., Yin, R., Deng, C., Chu, B., Nieminen, T., Kontkanen, J., Stolzenburg, D., Sipil\u00e4, M., Hussein, T., Paasonen, P., Bianchi, F., Salma, I., Weidinger, T., Pikridas, M., Sciare, J., Jiang, J., Liu, Y., Pet\u00e4j\u00e4, T., Kerminen, V. M., and Kulmala, M.: Sources and sinks driving sulphuric acid concentrations in contrasting environments: implications on proxy calculations, Atmos. Chem. Phys. Discuss., 2020, 1-24, 10.5194/acp-2020-155, 2020."]}

  • Other research product . Other ORP type . 2020
    Open Access
    Authors: 
    Juan Miguel Valverde; Riccardo De Feo; Artem Shatillo; Jussi Tohka;
    Publisher: Zenodo
    Project: EC | GenomMed (740264), AKA | Predictive brain image an... (316258), EC | GenomMed (740264), AKA | Predictive brain image an... (316258)

    MedicDeepLabv3+ trained models. For MedicDeepLabv3+ v1.1.0, please download trained_models_v1.1.0.zip

  • Open Access
    Authors: 
    Juan Miguel Valverde; Riccardo De Feo; Artem Shatillo; Jussi Tohka;
    Publisher: Zenodo
    Project: AKA | Predictive brain image an... (316258), EC | GenomMed (740264), AKA | Predictive brain image an... (316258), EC | GenomMed (740264)

    Official repository of MedicDeepLabv3+

  • Open Access English
    Authors: 
    Rossi, Tuomas; Erhart, Paul; Kuisma, Mikael;
    Publisher: Zenodo
    Project: AKA | Towards Nanoscale Organic... (295602), EC | RealNanoPlasmon (838996), AKA | Towards Nanoscale Organic... (295602), EC | RealNanoPlasmon (838996)

    This upload includes the codes and input scripts for reproducing the analysis presented in the article "Hot-Carrier Generation in Plasmonic Nanoparticles: The Importance of Atomic Structure" by Tuomas P. Rossi, Paul Erhart, and Mikael Kuisma. The codes reproduce the data of the article provided at doi:10.5281/zenodo.3927527. See README.md in the upload for a detailed description.

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