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In cooperative TF-TF binding, two transcription factors bind onto a shared DNA binding site as a pair. Previous work has demonstrated pairwise TF-TF-DNA interactions with position weight matrices (PWMs), which may however not sufficiently take into account the complexity and flexibility of pairwise binding. Results We propose two random forest (RF) methods for joint TF-TF binding site prediction: ComBind and JointRF. We train models with previously published large-scale CAP-SELEX DNA libraries, which comprise DNA sequences enriched for binding of a selected TF pair. JointRF builds a random forest with sub-sequences selected from CAP-SELEX DNA reads with previously proposed pairwise PWM. JointRF outperforms (area under receiver operating characteristics curve, AUROC, 0.75) the current state-of-the-art method i.e. orientation and spacing specific pairwise PWMs (AUROC 0.59). Thus, JointRF may be utilized to improve prediction accuracy for pre-determined binding preferences. However, pairwise TF binding is currently considered flexible; a pair may bind DNA with different orientations and amounts of dinucleotide gaps or overlap between the two motifs. Thus, we developed ComBind, which utilizes random forests by considering simultaneously multiple orientations and spacings of the two factors. Our approach outperforms (AUROC 0.78) PWMs, as well as JointRF (p<0.00195). ComBind provides an approach for predicting TF-TF binding sites without prior knowledge on pairwise binding preferences. However, more research is needed to assess ComBind eligibility for practical applications. Conclusions Random forest is well suited for modeling pairwise TF-TF-DNA binding specificities, and ComBind provides an improvement to pairwise binding site prediction accuracy."},"field_of_science":[{"id":"cfd80611-c263-4bde-bab8-11502ec390b5","url":"http://www.yso.fi/onto/okm-tieteenala/ta113","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Computer and information sciences","fi":"Tietojenkäsittely ja informaatiotieteet","sv":"Data- och informationsvetenskap"}}],"infrastructure":[],"issued":"1970-01-01","keyword":[],"language":[],"metadata_owner":{"id":"829302c3-f5d4-4d20-9ec3-5148bcf385cc","organization":"aalto.fi","admin_organization":"aalto.fi"},"other_identifiers":[],"persistent_identifier":"doi:10.6084/m9.figshare.c.6031779.v1","pid_generated_by_fairdata":false,"projects":[],"provenance":[],"relation":[],"remote_resources":[{"title":{"en":"Data in remote location","fi":"Aineisto ulkoisessa palvelussa","sv":"Material i en extern 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To this end we calculate the scattering and absorption efficiencies of oblate spheroidal CuSbS₂ nanoparticles using the surface integral equation method. We further investigate the optical response of thin layers containing CuSbS₂ spheroids at low volume fraction using a Monte Carlo method. We find that response of these layers can be considerably modified by changing the short axis length and the orientation of the particles within the layer with respect to the incoming radiation. This allows engineering the layers for specific polarization-dependent-response applications."},"field_of_science":[{"id":"f8d5f9ab-1c7d-4c5c-8ed5-e9ce964d798d","url":"http://www.yso.fi/onto/okm-tieteenala/ta114","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Physical sciences","fi":"Fysiikka","sv":"Fysik"}}],"infrastructure":[],"issued":"1970-01-01","keyword":[],"language":[],"metadata_owner":{"id":"829302c3-f5d4-4d20-9ec3-5148bcf385cc","organization":"aalto.fi","admin_organization":"aalto.fi"},"other_identifiers":[],"persistent_identifier":"doi:10.6084/m9.figshare.c.6000049.v2","pid_generated_by_fairdata":false,"projects":[],"provenance":[],"relation":[],"remote_resources":[{"title":{"en":"Data in remote location","fi":"Aineisto ulkoisessa palvelussa","sv":"Material i en extern tjänst","und":"Data in remote 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integer between 280000 - 319999)\r\n\t\tthe 2nd column:                          Observation (an integer):\r\n\t\t\r\n\t\t\tMeasurement frequency: 7.953 MHz\r\n\t\t\tData rate:                         1000 data points per a second\r\n\t\t\r\n\t\t\r\n\t\r\n\t\r\n\r\n\r\n \r\n\r\n\r\n\tThe file prepared by Esa Kallio (esa.kallio@aalto.fi), Aalto University, Finland, on Sep. 8, 2022\r\n\r\n\r\n \r\n\r\n\r\n\tMiscellanous:\r\n\r\n\r\n           (the number of the data point, -observation) plots can be found from the publication\r\n\r\n           Kallio et al., Radar – CubeSat Transionospheric HF Propagation Observations: Suomi 100 - Satellite and EISCAT HF Facility, Radio Science."},"field_of_science":[{"id":"8aaa6f8d-a5ad-4a23-8d26-1d76c279e2f8","url":"http://www.yso.fi/onto/okm-tieteenala/ta115","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Astronomy, Space science","fi":"Avaruustieteet ja tähtitiede","sv":"Rymdvetenskap och 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Opetus- ja kulttuuriministeriön osatukemassa hankkeessa kartoitettiin sopivinta mallintamistekniikkaa museon kokoelmissa oleville tanssipuvuille. Osana hanketta Aalto-yliopiston Rakennetun ympäristön mittauksen ja mallintamisen instituutti MeMo:ssa testattiin puvun mallintamista fotogrammetrialla, strukturoidun valon skannerilla sekä laserkeilaimella. Testausten perusteella arvioitiin, että fotogrammetria oli lupaavin metodi pukujen mallintamiseen. \r\nHankkeen toisessa vaiheessa museo osti mallintamispalvelua kaupalliselta toimijalta, ja yhteensä 15 pukua mallinnettiin fotogrammetrialla.\r\n\r\nTeatterimuseon hankeraportin voi ladata luettavaksi osoitteesta\r\nhttps://www.teatterimuseo.fi/fi/3D-malleja-Teatterimuseon-tanssipuvuista\r\n\r\nTeatterimuseon Sketchfab-tili https://sketchfab.com/Theatre_Museum .\r\n\r\nAineistossa esiintyvän puvun tiedot / Information on the modeled costume:\r\n\r\nBalettipuku, tutu / Ballet costume, tutu.\r\nTeos / Title: Prinsessa Ruusunen / Sleeping Beauty\r\nTuotanto / Production: Suomen kansallisooppera (nyk. Suomen kansallisooppera ja -baletti) / Finnish National Opera (now the Finnish National Opera and Ballet) 1999\r\nKoreografi / Choreographer: Rudolf Nurejev (Marius Petipan mukaan / According to Marius Petipa)\r\nSäveltäjä / Composer: Pjotr Tšaikovski / Pyotr Ilyich Tchaikovsky\r\nPukusuunnittelu / Costume design: Erika Turunen\r\nTanssijat / Dancers: Alexandra Campbell ja/and Asta Lindholm\r\nRooli / Role: Ruususen ystävätär / Aurora’s friend\r\n\r\nPrinsessa Ruusunen -baletin ensi-ilta oli 26.3.1999. Se oli yksi pukusuunnittelija Erika Turusen varhaisimmista oopperalle suunnittelemista teoksista. Tämän jälkeen hän on toiminut Suomen kansallisoopperan ja -baletin päätoimisena pukusuunnittelijana jo yli 20 vuotta. Hän on suunnitellut pukuja myös nykytanssiteoksiin. (https://www.erikaturunen.com)\r\nMallinnettu tutu on ollut myös Suomen Kansallisoopperan balettioppilaitoksen oppilaiden käytössä. Alun perin pukuun on kuulunut myös kullanvärinen, helmikoristeinen päähine. Puku kuuluu Teatterimuseon opetuskokoelmaan."},"field_of_science":[{"id":"be6042ba-672d-4271-88a9-836126561f67","url":"http://www.yso.fi/onto/okm-tieteenala/ta1171","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Geosciences","fi":"Geotieteet","sv":"Geovetenskaper"}}],"infrastructure":[],"issued":"2021-12-07","keyword":[],"language":[],"metadata_owner":{"id":"829302c3-f5d4-4d20-9ec3-5148bcf385cc","organization":"aalto.fi","admin_organization":"aalto.fi"},"other_identifiers":[],"persistent_identifier":"doi:10.5281/zenodo.5776368","pid_generated_by_fairdata":false,"projects":[],"provenance":[],"relation":[],"remote_resources":[{"title":{"en":"Data in remote location","fi":"Aineisto ulkoisessa palvelussa","sv":"Material i en extern tjänst","und":"Data in remote location"},"use_category":{"id":"1ad1b146-d147-45db-a2fd-1096abc94984","url":"http://uri.suomi.fi/codelist/fairdata/use_category/code/source","in_scheme":"http://uri.suomi.fi/codelist/fairdata/use_category","pref_label":{"en":"Source material","fi":"Lähdeaineisto"}},"download_url":"https://zenodo.org/api/records/5776369"}],"spatial":[],"state":"published","temporal":[],"theme":[],"title":{"en":"Tutu 3D"},"created":"2025-12-04T07:56:15Z","modified":"2026-03-26T06:39:13Z","dataset_versions":[{"id":"2af15aa0-9edf-4280-a15d-1249b61a69c3","title":{"en":"Tutu 3D"},"persistent_identifier":"doi:10.5281/zenodo.5776368","state":"published","created":"2025-12-04T07:56:15Z","version":1}],"published_revision":2,"version":1,"api_version":3,"metadata_repository":"Fairdata"},{"id":"a19259e8-abaa-4403-b1db-9540095c052b","access_rights":{"id":"df12dcd7-6c26-4271-8899-fffdcd0075d0","license":[{"id":"add72c17-4fca-4d00-a2c7-b849c424c42f","url":"http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0","in_scheme":"http://uri.suomi.fi/codelist/fairdata/license","pref_label":{"en":"Creative Commons Attribution 4.0 International (CC BY 4.0)","fi":"Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"}}],"access_type":{"id":"b41462f7-00bf-4e50-935b-2bf1184453a7","url":"http://uri.suomi.fi/codelist/fairdata/access_type/code/open","in_scheme":"http://uri.suomi.fi/codelist/fairdata/access_type","pref_label":{"en":"Open","fi":"Avoin"}},"restriction_grounds":[]},"actors":[{"id":"35a711e2-e512-4fb9-a2d0-0035113c8385","roles":["creator"],"person":{"id":"86e3009e-6b92-4d84-8c81-c43ec70236ac","name":"Jussi Juola","external_identifier":"https://orcid.org/0000-0002-6050-7247"},"organization":{"id":"3ee7a70d-b976-4a70-b243-1c5504cd0247","pref_label":{"en":"Department of Built Environment","fi":"Department of Built Environment","sv":"Department of Built Environment","und":"Department of Built Environment"},"url":"http://uri.suomi.fi/codelist/fairdata/organization/code/10076-T213","in_scheme":"http://uri.suomi.fi/codelist/fairdata/organization","parent":{"id":"2f9f9011-4061-4a93-96af-768471abada7","pref_label":{"en":"Aalto University","fi":"Aalto-yliopisto","sv":"Aalto-universitetet","und":"Aalto-yliopisto"},"url":"http://uri.suomi.fi/codelist/fairdata/organization/code/10076","in_scheme":"http://uri.suomi.fi/codelist/fairdata/organization"}}},{"id":"9aefc31e-497f-4e06-9efd-9b4b7fb16e4e","roles":["creator"],"person":{"id":"17456d54-9f8f-42f2-a579-84f9e2d49483","name":"Miina Rautiainen","external_identifier":"https://orcid.org/0000-0002-6568-3258"},"organization":{"id":"3ee7a70d-b976-4a70-b243-1c5504cd0247","pref_label":{"en":"Department of Built Environment","fi":"Department of Built Environment","sv":"Department of Built Environment","und":"Department of Built Environment"},"url":"http://uri.suomi.fi/codelist/fairdata/organization/code/10076-T213","in_scheme":"http://uri.suomi.fi/codelist/fairdata/organization","parent":{"id":"2f9f9011-4061-4a93-96af-768471abada7","pref_label":{"en":"Aalto University","fi":"Aalto-yliopisto","sv":"Aalto-universitetet","und":"Aalto-yliopisto"},"url":"http://uri.suomi.fi/codelist/fairdata/organization/code/10076","in_scheme":"http://uri.suomi.fi/codelist/fairdata/organization"}}},{"id":"5b93e1be-bf38-4c71-8d6d-2e9b9c8089bf","roles":["publisher"],"organization":{"id":"851fc3f9-5815-4cff-a7e6-817a9c8ac569","pref_label":{"en":"Mendeley Data","fi":"Mendeley Data","sv":"Mendeley Data"}}}],"cumulative_state":0,"data_catalog":"urn:nbn:fi:att:data-catalog-acris","description":{"en":"The methods used to collect and preprocess this dataset have been reported in detail in Juola J., Hovi A., Rautiainen M., 2022. A spectral analysis of stem bark for boreal and temperate tree species. Ecology and Evolution. DOI:10.1002/ece3.8718\r\n\r\nThe dataset includes stem reflectance spectra of standing dead trees for the species of Scots pine (Pinus sylvestris L.). We measured hemispherical-directional reflectance factors (HDRF) of stem samples. The data were measured using a Specim IQ imaging spectrometer. The measurements were taken from the northern side of the stem at breast height (1.3 m), and the image acquisition distance was 20 cm. The imaging spectrometer operates in the visible and near-infrared wavelength region (400–1000 nm). The measurements were made in the municipality of Rovaniemi, Finland. We measured 13 standing dead Scots pine trees, accounting to a total of 13 unique stem samples. One sample refers to a hyperspectral reflectance image taken of a single standing dead tree stem (at 1.3 m height). The 13 mean spectral signatures (presented in this dataset) were calculated for each sample by averaging the HDRF values over all pixels per wavelength. The measurements were conducted in the beginning of August 2022. All measurements were made under diffuse illumination conditions and the images were taken in perpendicular view-angle to the standing stem. The dataset includes 1) one tabular file that contains all 13 mean reflectance spectra, and 2) a supportive document that has images of the individual standing dead trees and RGB visualizations of the measured hyperspectral reflectance images.\r\n\r\nThe spreadsheet (.csv) is organized as follows: first two rows that start with hashtag (#) contain comments for citing, first column \"tree_species\" (standing_dead_tree_pinus_sylvestris) indicates the standing dead tree species, second column \"id\" (K1-K13) indicates the unique stem id's for which images can be found in the supportive document, and the subsequent columns \"wl397.32\"-\"wl1003.58\" indicate the measured HDRF value at that wavelength. The encoding of the csv file is UTF-8. \r\n\r\nThe supportive document (.pdf) contains the dataset description given here, but also images of the standing dead trees taken in the forest and their corresponding RGB visualizations of the measured hyperspectral reflectance images. The Diameter at Breast Height (DBH) are given for each stem in the figure descriptions."},"field_of_science":[{"id":"be6042ba-672d-4271-88a9-836126561f67","url":"http://www.yso.fi/onto/okm-tieteenala/ta1171","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Geosciences","fi":"Geotieteet","sv":"Geovetenskaper"}}],"infrastructure":[],"issued":"2022-09-21","keyword":[],"language":[],"metadata_owner":{"id":"829302c3-f5d4-4d20-9ec3-5148bcf385cc","organization":"aalto.fi","admin_organization":"aalto.fi"},"other_identifiers":[],"persistent_identifier":"doi:10.17632/8dvx3vvvk9.1","pid_generated_by_fairdata":false,"projects":[],"provenance":[],"relation":[],"remote_resources":[],"spatial":[],"state":"published","temporal":[],"theme":[],"title":{"en":"A dataset of stem reflectance spectra for standing dead Scots pine trees"},"created":"2025-12-04T07:56:12Z","modified":"2026-03-26T06:39:11Z","dataset_versions":[{"id":"a19259e8-abaa-4403-b1db-9540095c052b","title":{"en":"A dataset of stem reflectance spectra for standing dead Scots pine trees"},"persistent_identifier":"doi:10.17632/8dvx3vvvk9.1","state":"published","created":"2025-12-04T07:56:12Z","version":1}],"published_revision":2,"version":1,"api_version":3,"metadata_repository":"Fairdata"},{"id":"7ffa7603-69d6-4756-95bc-9450a58e53b6","access_rights":{"id":"f1ee5917-a526-4234-b172-ad29ae3b7fb8","license":[{"id":"5a00a777-42a2-41a9-9911-968146f7e53f","url":"http://uri.suomi.fi/codelist/fairdata/license/code/other","in_scheme":"http://uri.suomi.fi/codelist/fairdata/license","pref_label":{"en":"Other","fi":"Muu"}}],"access_type":{"id":"b41462f7-00bf-4e50-935b-2bf1184453a7","url":"http://uri.suomi.fi/codelist/fairdata/access_type/code/open","in_scheme":"http://uri.suomi.fi/codelist/fairdata/access_type","pref_label":{"en":"Open","fi":"Avoin"}},"restriction_grounds":[]},"actors":[{"id":"44ac754f-3319-4211-b9ff-e01f8af63538","roles":["creator"],"person":{"id":"135316d7-da4e-4080-89f0-fb89320f3447","name":"Marko Kallio","external_identifier":"https://orcid.org/0000-0002-6917-7790"},"organization":{"id":"3ee7a70d-b976-4a70-b243-1c5504cd0247","pref_label":{"en":"Department of Built Environment","fi":"Department of Built Environment","sv":"Department of Built Environment","und":"Department of Built Environment"},"url":"http://uri.suomi.fi/codelist/fairdata/organization/code/10076-T213","in_scheme":"http://uri.suomi.fi/codelist/fairdata/organization","parent":{"id":"2f9f9011-4061-4a93-96af-768471abada7","pref_label":{"en":"Aalto University","fi":"Aalto-yliopisto","sv":"Aalto-universitetet","und":"Aalto-yliopisto"},"url":"http://uri.suomi.fi/codelist/fairdata/organization/code/10076","in_scheme":"http://uri.suomi.fi/codelist/fairdata/organization"}}},{"id":"b1714d9d-0b7a-43a9-a9a1-6131570b3c54","roles":["publisher"],"organization":{"id":"f94a8099-1e84-467a-b822-98998f480e52","pref_label":{"en":"Zenodo","fi":"Zenodo","sv":"Zenodo"}}}],"cumulative_state":0,"data_catalog":"urn:nbn:fi:att:data-catalog-acris","description":{"en":"# GMD_hydrostreamer\r\nCode and (part of) the data needed to replicate the figures in the hydrostreamer 1.0 model description paper: https://doi.org/10.5194/gmd-2020-276\r\nThe code reproduces figures 3-5, table 4 and appendix tables A1 to A4. Results.zip contains downscaled and routed outputs from the 15 runoff datasets for each river segment.\r\n\r\nThe repository contains all data needed except for monitoring data, for which our license does not cover distribution.\r\nThe data is available from https://portal.mrcmekong.org. *Note that the code does not run completely without the observations.*\r\n\r\nOther data included are:\r\n* runoff datasets obtained from the ISIMIP archive (https://esg.pik-potsdam.de/search/isimip/), and cropped to the area-of-interest\r\n* discharge data obtained from the ISIMIP archive, and cropped to the area-of-interest\r\n* GRADES data for the 10 monitoring stations included, aggregated to monthly means. https://doi.org/10.1029/2019WR025287\r\n* GLOFAS data for the 10 monitoring stations included, aggregated to monthly means. https://cds.climate.copernicus.eu/cdsapp#!/dataset/cems-glofas-historical\r\n* HydroSHEDS river network for the area-of-interest. https://hydrosheds.org\r\n* River segment specific catchment areas delineated using a Voronoi Diagram, and using HydroSHEDS drainage direction raster.\r\n* Station locations for the 0.5 degree data, including the HydroSHEDS river segment ID for each station.\r\n\r\nThe ISIMIP data is distributed with CC-BY 4.0 or CC-NY-NC 4.0 license. Refer to the following link for which license applies to which model. https://www.isimip.org/gettingstarted/terms-of-use/licenses-publicly-available-isimip-data/?query=license#licences-for-isimip2a\r\nGRADES data can be only used for research purposes.\r\n\r\nThe title and description of this software correspond with the situation when the software metadata was imported to ACRIS. 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Each of them were measured using an omnidirectional sound source and 5 sound receivers. For each configuration, 5 IRs were captured. The total number of measurements in the dataset is 132 037.\r\n\r\nFor more information and the reverberation time values estimated from the IRs, please see the paper \"Calibrating the Sabine and Eyring formulas\" by Karolina Prawda, Sebastian J. Schlecht, and Vesa Välimäki, in The Journal of the Acoustical Society of America\r\n\r\nThe work leading to producing the dataset and related research was supported by the Nordic Sound and Music Computing Network---NordicSMC, NordForsk project number 86892.\r\n\r\n \r\n\r\nHow to read the files in the dataset:\r\n\r\nThe general style of file naming is:\r\nIR_numClosed_NumberOfReflectivePanels_numComb_CombinationNumber_mic_ReceiverNumber_sweep_SweepNumber\r\nfor example, for 1 reflective panel, combination 87, IR obtained from 3rd out of 5 sweeps recorded by microphone number 2, the filename is:\r\nIR_numClosed_1_numComb_87_mic_2_sweep_3.wav\r\n\r\nThe dataset was divided into several files due to its total size. The files included in each .zip file are indicated in its name.\r\n\r\nIf some of the sound files are missing, e.g. for a certain combination and microphone there are 4 IR recordings instead of 5, it means that the sweep was discarded in the pre-processing phase due to non-stationary noise.\r\nRead more: Karolina Prawda, Sebastian J. Schlecht, and Vesa Välimäki, \"Robust selection of clean swept-sine measurements in non-stationary noise\", The Journal of the Acoustical Society of America 151, 2117-2126 (2022), doi: https://doi.org/10.1121/10.0009915\r\n\r\nThe specific combinations with indication whether the panel was in a reflective (represented by figure 0) or an absorptive (represented by figure 1) state are listed in combinations_setup.csv file.\r\nThe first column contains the combination number (0--5341), the first row is the panel number (1--55).\r\n\r\nArni_panels_numbers.pdf contains a diagram showing the panel numbers and locations.\r\n\r\nArni_layout.jpg contains a drawing specifying the positions of source source, sound receivers, and other elements of the interior."},"field_of_science":[{"id":"fd80ad86-b461-4ffb-abbd-888bc2ffd653","url":"http://www.yso.fi/onto/okm-tieteenala/ta213","in_scheme":"http://www.yso.fi/onto/okm-tieteenala/conceptscheme","pref_label":{"en":"Electronic, automation and 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