Crc April 2022

crc@lists.oulu.fi

12 participants
43 discussions

Reminder: Short questionnaire about doing research
by Salla Kangas 25 Apr '22

25 Apr '22

Dear all, We would like to hear about your experiences and thoughts about replicating your experiments before the FIRN morning coffee event on Friday 29th April (details below). We are interested in your answers regardless of your event attendance. The questionnaire is open until Thursday 2 pm on April 28th Answer the questionnaire here: https://forms.office.com/Pages/ResponsePage.aspx?id=WXWumNwQiEKOLkWT5i_j7s_… You are also still welcomed to register this event (DL is today!). Thank you for your input! BR, Salla Kangas ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Reproducibility morning café event on Friday 29th April at 8:30 o'clock, you can participate on-site (Kontinkangas Tellus meeting room Carpi), or via Zoom The Finnish Reproducibility Network (FIRN) (https://www.finnish-rn.org/) is a national peer-led consortium that promotes scientific integrity and open science for better reproducibility. Reproducibility Network activities are currently being established around the world. The aim is to improve the quality of research by dissemination of the knowledge within the scientific community on factors that are essential for reproducibility and replicability. FIRN activities in Oulu are discussed on reproducibility morning café event on Friday 29th April at 8:30 o'clock, and we invite everyone who is interested on this topic to participate on site (Kontinkangas Tellus meeting room Carpi), or via Zoom. In this first event, we will hear what FIRN is, and we will discuss what kind of activities, such as events, training and courses, we should have here at the University of Oulu. These activities are aimed to all the staff and students who want to learn how to make better science. Welcome! Program: 8:30 Coffee is served 8:45 What is FIRN for? Presentation by Vootele Vöikar (NC, HiLIFE) and Andreas Scherer (FIMM, HiLIFE) 9:15-10 Discussion on reproducibility and good scientific practices -What kind of support and training is needed in Oulu? Please, send registration email to salla.kangas(a)oulu.fi<mailto:salla.kangas@oulu.fi> stating whether you wish to attend on-site or remotely by Monday 25th of April. Thank you! The event is organized with the Unit for Strategy and Science Policy, University of Oulu. You can also follow Finnish Reproducibility Network in Twitter to learn more about reproducibility and the Network's activities: https://twitter.com/FinRepro

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Kysymys vasta-aineista
by Antti Haapalainen 25 Apr '22

25 Apr '22

Hei, Olisko kellään lainata: b-actin tai GAPDH kanin primääri vasta-ainetta? Terv. Antti

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Brown Bag Seminar: What can cells and molecules tell us about the world?
by Essi Erkkilä 25 Apr '22

25 Apr '22

Dear all, Our next Brown Bag seminar takes place on Wed 27th of April from 11 to 12. The event is organized live at the Tellus Linnanmaa Stage, but it is also possible to participate remotely. Note that today is the last day to register for the live event! For live participation, please register here by 4 p.m.: https://link.webropolsurveys.com/Participation/Public/aaaab7cf-138b-40db-a1… You are welcome to attend the live event even if you haven't registered, but lunch will be reserved for registered participants only. Remote participation is in Zoom: https://oulu.zoom.us/j/68736999744. The event is held in English. The speakers in this Brown Bag seminar will be Daniela Ungureanu, associate professor in the disease networks research unit (Faculty of Biochemistry and Molecular Medicine) contributing to the Fibrobesity profiling theme, and Janne Koskimäki, a postdoctoral researcher from the Ecology and genetics research unit working with Host-Microbe Interactions. In the Brown Bag seminars of Spring 2022, you will get the chance to get to know the research of the Fibrobesity profiling theme alongside interesting research topics from other disciplines in our university. Fibrobesity is an Academy of Finland funded research theme that focuses on obesity-related fibrotic pathologies. On behalf of the Fibrobesity Team, Essi Erkkilä --------------------------------------------------------------------------------------- Essi Erkkilä Communications Specialist, Profi6 Fibrobesity Research Unit for Internal Medicine (Room S5 224) Faculty of Medicine University of Oulu tel. +358 50 521 5852 Twitter: FibroHealthOulu @FibroOulu FibroHealth - Combatting Fibrosis in Chronic Diseases | University of Oulu<https://www.oulu.fi/en/fibrohealth-combatting-fibrosis-chronic-diseases> [cid:image001.jpg@01D85899.A27189A0]

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Minerva Foundation Medix Prize, Gräsbeck-grant and Selander-grant
by Anne Vainionpää 25 Apr '22

25 Apr '22

FYI Minerva Foundation announcement of prize and grants. Documents are in English. Deadline May 2. From: Cia Olsson <cia.olsson(a)minervainstitute.fi> Sent: maanantai 25. huhtikuuta 2022 9.49 To: Anne Vainionpää <anne.vainionpaa(a)oulu.fi> Subject: Haku käynnissä: Minervasäätiön Medix-palkinto, Gräsbeck-stipendi ja Selander-apuraha Minervasäätiön Medix-palkinto, Gräsbeck -stipendi sekä Selander-rahaston apurahat ovat haettavissa 2.5.2022 asti. Liitteenä tiedot hauista sekä word- että PDF-tiedostona. Yt. Cia Olsson Cia Olsson Laboratoriopäällikkö Lääketieteellinen Tutkimuslaitos Minerva BIOMEDICUM Helsinki 2U Tukholmankatu 8 00290 Helsinki puh. +358 50 4487771 s-posti: cia.olsson(a)minervainstitute.fi<mailto:cia.olsson@minervainstitute.fi> <http://www.helsinki.fi/minerva> www.minervainstitute.fi<http://www.minervainstitute.fi>

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Innovative health initiative (IHI): Call information and brokerage event on 14 June 2022
by Johanna Kallio 25 Apr '22

25 Apr '22

Dear all, For your information. The Innovative Health Initiative (IHI) plans to launch the first calls in June 2022. IHI will organize an information and brokerage event on 14 June in a hybrid format, Brussels and online. Participation in the one-day event is free of charge. However, registration and profile activation are required to attend the brokerage event. More information about the event: https://www.ihi.europa.eu/news-events/events/ihi-kick-and-brokerage-event The draft topic texts have been published on the IHI website to give applicants additional time to start building consortia and draft proposals. All information is indicative and subject to change. The proposed themes focus on cancer, cardio-metabolic diseases, neurodegenerative diseases, as well as more technology-focused themes on health data and the development of health technologies. More information about the call topics: https://www.ihi.europa.eu/apply-funding/future-opportunities Br, Johanna ------------------------------------------------------------------------- Johanna Kallio, D.Sc. (Tech) Tutkimusrahoitusasiantuntija | Research funding specialist Oulun yliopisto | University of Oulu Tel. +358 29 448 5414 Mobile +358 50 479 2506 Email johanna.kallio[at]oulu.fi

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Reminder, today: HBS-DP Research Plan Seminar, starting at 14:00, online
by Mirja Peltola 25 Apr '22

25 Apr '22

Reminder, today HEALTH AND BIOSCIENCES DOCTORAL PROGRAMME - RESEARCH PLAN SEMINAR<https://www.oulu.fi/en/science-arctic-attitude/graduate-school/organisation…> Time: Monday 25.4.2022, starting at 14:00 Place: online, zoom-link >>><https://oulu.zoom.us/j/66066770271> Research plan presentations by doctoral researchers: 14:00 - 14:20 Yiyan He Research Plan: Dynamic mechanism of noise exposure and obesity Research Unit: Center for Life Course Health Research Supervisor: Sylvain Sebert 14:20 - 14:40 Sami Raatikainen Research Plan: Cardiotrophin-1 A92T mutations effects on cardiac fibrosis and cardiotoxicity of kinase inhibitors Research Unit: Biomedicine Supervisor: Risto Kerkelä 14:40 - 15:00 Mervi Kreus Research Plan: Extracellular matrix proteins and NHLRC2 in idiopathic pulmonary fibrosis and lung cancer Research Unit: Internal Medicine Supervisor: Riitta Kaarteenaho 15:00 - 15:20 Topias Karjula Research Plan: Clinical and Pathological prognostic factors of pulmonary metastases from colorectal carcinoma Research Unit: Surgery, Aenesthesia and Intenstive Care Supervisor: Olli Helminen Best wishes, Mirja ------------------------------------------------------------------------------------------------------ Mirja Peltola, PhD, BSc (Tech.) Koordinaattori | Coordinator Oulun yliopisto | University of Oulu Terveys- ja biotieteiden tohtoriohjelma | Health and Biosciences Doctoral Programme Tel. 0294 48 5447 PO Box 5000, FI-90014 OULUN YLIOPISTO (Aapistie 5A, Room 476B) www.oulu.fi<http://www.oulu.fi/yliopisto> www: Terveys- ja biotieteiden tohtoriohjelma | Health and Biosciences Doctoral Programme<https://www.oulu.fi/en/science-arctic-attitude/graduate-school/organisation…>

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Image analysis book & QuPath jobs, webinar & hackathon
by Sanna Palosaari 24 Apr '22

24 Apr '22

FYI ----- Hi, I'd like to share three announcements - involving two job advertisements, a webinar, a hackathon, and new textbook - all connected to bioimage analysis & open software. I'd appreciate it if you could take a look, and share the information with anyone else you think might be interested. Thanks! Pete 1. New open textbook: Introduction to Bioimage Analysis I recently released a new image analysis textbook at https://bioimagebook.github.io It's not really a normal textbook: it's a free, open, interactive 'executable book' containing text, illustrations, videos, quizzes and live code. It covers not only the main concepts and techniques of image analysis, but also how they are applied in software - particularly ImageJ/Fiji and Python. I wrote the book with biologists in mind, but it's intended for anyone with an interest in the topic - either as a student or a teacher. You can find a brief overview and videos showing it in action here on Twitter<https://twitter.com/petebankhead/status/1516729400137551878?s=20&t=KBYJ5qRm…>. 2. Two open positions (Postdoc / Research Software Engineer) A goal of the book is to facilitate cross-disciplinary research by making image analysis more accessible and understandable for people with different expertise. Another way my group tries to do that is through open algorithms and software. In that regard, there are two new positions to join me in working on QuPath (http://qupath.github.io): * QuPath position 1 - focus on core software, handling huge images, image analysis<https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/job/3974> * QuPath position 2 - focus on user experience, data visualization<https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/job/4009> Both would be suitable for either a postdoc with strong coding skills or a research software engineer. There's more information on the project here<https://chanzuckerberg.com/eoss/proposals/qupath-boosting-bioimage-analysis…>. I may be a bit biased, but I think that these positions offer a particularly exciting opportunity to apply computational skills in a way that can directly benefit a large number of research projects worldwide. I base this on the fact that, with >200k downloads<https://github.com/qupath/qupath> and >1.2k citations<https://doi.org/10.1038/s41598-017-17204-5>, QuPath is already one of the most widely-used software applications for bioimage analysis. Use is increasing quickly (~2/3 of the citations are since 2021), and there's a very active user community with over 2,000 QuPath discussions<https://forum.image.sc/tag/qupath> on the Scientific Community Image Forum. There's also a growing developer community, with projects like PAQUO: PAthological QUpath Obsession<https://github.com/bayer-science-for-a-better-life/paquo>, WarPy<https://forum.image.sc/t/warpy-registration-of-whole-slide-images-at-cellul…> and QuPath Edu<https://github.com/yli-hallila/qupath-edu-extension> building on QuPath's openness in creative ways. QuPath's future development has recently been awarded funding from CZI (Essential Open Source Software for Science) and the Wellcome Trust (Technology Development Grant) - so whoever joins will be part of a growing team dedicated to image analysis and open science, with the funding and flexibility to work on solving some of the biggest challenges in biological and biomedical image analysis. To get an idea of what QuPath can already do, check out the YouTube channel<http://youtube.com/c/qupath> or follow us on Twitter<https://twitter.com/qupath> - but I hope that together we can make it do even more. 3. QuPath webinar & hackathon Finally: I realise it's a bit late to mention, but I'll be giving two new QuPath webinars on 25 April (to cater for different timezones) * QuPath: Past, Present and Future - 9am (BST)<https://teams.microsoft.com/registration/sAafLmkWiUWHiRCgaTTcYQ,lCxQUFpGhUi…> / 11am (Finland) * QuPath: Past, Present and Future - 6pm (BST)<https://teams.microsoft.com/registration/sAafLmkWiUWHiRCgaTTcYQ,lCxQUFpGhUi…> / 8pm (Finland) Throughout the rest of the week, anyone interested in the programming side of QuPath can join in a hackathon as well. Beyond its graphical interface, QuPath is extensible and scriptable - so the hackathon will be a chance for people who are comfortable writing code to learn how to get even more out of the software. You can find more details about both these events at https://forum.image.sc/t/april-2022-qupath-webinar-hackathon/65779 Peter Bankhead Senior Lecturer p.bankhead(a)ed.ac.uk<mailto:p.bankhead@ed.ac.uk> Institute of Genetics and Cancer University of Edinburgh Western General Hospital, Crewe Road Edinburgh, EH4 2XU The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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Soluviljelijöiden kokous huhtikuu 2022
by Reetta Hinttala 22 Apr '22

22 Apr '22

Hei, lyhyt yhteenveto tämän viikon kokouksesta. Hyvää viikonloppua, Reetta CRC:n soluviljelijöiden kokous ti 19.4.22 Yhteenveto 1. Uusi nestetyppisäiliö on nyt toimintakunnossa ja sitä voidaan alkaa täyttää. Säiliön yhteyteen perustetaan perinteinen kansio johon merkitään tarkemmin rackien ja boxien sisältö. Sen lisäksi on sähköiseen kansioon S:\KLIIN\CRC\Nestetyppitankit Liquid nitrogen tanks tiedostoon luotu excel-lehti (Locator VI) johon merkitään varaustilanne tutkimusryhmittäin. Ihotaudit siirtää omat soluampullit tankkiin varaten yhden kokonaisen rackin. Tärkeää huomioida, että huone on nyt täysi eikä sinne mahdu enää uutta nestetyppitankkia. Kannattaa siis täyttää tilaa harkiten ja poistaa aika ajoin ampullit joiden säilytys ei ole tarpeellista. 2. 341/342B laboratorioiden eteistilassa oleva fuugi on rikki. Laitetta yritetään korjata parhaillaan ja tarvittaessa tilalle hankitaan uusi. Gyne on tarjonnut väliaikaisesti klinikasta fuugin käyttöömme syksyyn saakka. Tällä hetkellä fuugista puuttuvat 50 ml:n falconeiden adapterit, 15 ml:n putkien fuugaus onnistuu. Kiitos paljon Riikka! 3. Seuraava kokous ti 14.6. klo 9 joko etänä tai CRC:n kahvihuoneessa. CRC Cell Culture Meeting Tue 19.4.22 Summary 1. The new liquid nitrogen tank is now cooled and operational. A folder is placed next to the tank, in which the contents of the racks and boxes will be marked by hand. In addition, an excel sheet has been created in the electronic folder S: \ KLIIN \ CRC \ Liquid nitrogen tanks. Dermatology group transfers their cell ampoules to the tank, reserving one rack. It is important to note that the room is now full and there is no space for another liquid nitrogen tank. It is therefore important to fill the space carefully and remove ampoules from time to time which do not require storage. 2. The centrifuge in the entry room of 341 / 342B laboratories is broken. It is currently under repair, a new one will be purchased if necessary. Gyne has kindly provided us a temporary fuge from their clinic until the Fall. Currently, we lack adapters for 50 ml falcon tubes, but 15 ml tubes can be centrifuged. Thank you very much Riikka! 3. Next meeting Tue 14.6. at 9 a.m. either remotely or in CRC's coffee room. From: cellcrc-bounces(a)lists.oulu.fi <cellcrc-bounces(a)lists.oulu.fi> On Behalf Of Reetta Hinttala Sent: torstai 3. maaliskuuta 2022 13.39 To: cellcrc(a)lists.oulu.fi; 'crc(a)lists.oulu.fi' <crc(a)lists.oulu.fi> Subject: [Cellcrc] Soluviljelijöiden kokous helmikuu 2022 Hei, tässä yhteenveto soluviljelijöiden kokouksesta. t.Reetta CRC:n soluviljelijöiden kokous to 24.2.22 Yhteenveto 1. Uusi nestetyppisäiliö saapunut soluampulleille. Säiliötä täytetään ja jäähdytetään pikkuhiljaa nestetypellä täyttämällä muutaman viikon ajan ennen sen käyttöönottoa. Tarvittaessa tilataan nestetypen lisätäyttö. Säiliön yhteyteen perustetaan kansio johon merkitään tarkemmin rackien ja boxien sisältö. Sen lisäksi on sähköiseen kansioon S:\KLIIN\CRC\Nestetyppitankit Liquid nitrogen tanks tiedostoon luotu uusi excel-lehti (Locator VI) johon merkitään varaustilanne tutkimusryhmittäin. Tärkeää on, että ryhmät saavat solut säilytykseen ja että tilaa jaetaan kokonaisuus huomioon ottaen. Erityisesti huomioidaan ihotautien ryhmän tilantarve koska heillä ei ole säilytystilaa CRC:n aiemmin hankituissa yhteisissä tankeissa. 2. 341B soluviljelyn laminaarin suodatin on vaihdettu ja laminaaria voi jälleen käyttää. Loppuraportti Kojairin tekemästä tarkastuksesta puuttuu vielä. 3. Kokouksessa keskusteltiin tulossa olevasta IV koneen huollosta. Soluviljelyiden laminaarit ovat kaikki toiminnassa tuolloin ma 7.3. ja käyttökatkos koskee ainoastaan CRC:n osalta ilmanvaihtoa kahvihuoneen ja Biocenterin lasiovien välisellä alueella. 4. Anja ottaa vastaan näytteitä mykoplasmatestiin tiistaihin 15.3. saakka. 5. Seuraava kokous ti 19.4. klo 9 joko etänä tai CRC:n kahvihuoneessa. CRC Cell Culture Meeting Tue 19.10.21 Summary 1. A new liquid nitrogen tank has arrived for cell ampoules. The tank is gradually filled and cooled with liquid nitrogen for a few weeks before use. If necessary, extra liquid nitrogen is ordered. A folder is located next to the tank, in which the contents of the racks and boxes will be marked by hand. In addition, an excel sheet has been created in the electronic folder S: \ KLIIN \ CRC \ Liquid nitrogen tanks. It is important that there is enough storage space for researchers who need it and that the space is distributed based on equal principles. Particularly this applies to the dermatology group, who does not have any slots in older LN tanks of CRC. 2. The filter for laminar in 341B has been replaced and the laminar can be used again. The final report of Kojair's inspection is still missing. 3. We discussed the upcoming air conditioning maintenance on Mon 7.3. Cell culture laminars are all operational on that day and the maintenance only applies to ventilation in the area between the coffee room and the glass doors of the Biocenter. 4. Anja will run mycoplasma test in March. You can bring samples to her until Tue 15th of March. 5. Next meeting Tue 19.4. at 9 a.m. either remotely or in CRC's coffee room.

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KUTSU tutkijayhteisölle Future clinical trials konferenssi 7-8.6.2022 (Hki ja hybridi)
by Riipinen Katja 22 Apr '22

22 Apr '22

Tiedoksi: Future Clinical trials - from tomorrow to 2030 - Why choose the Nordics? Aika: 7.-8.6.2022 Paikka: Team Finland -talo (Porkkalankatu 1, Helsinki). Tapahtumaa on mahdollista seurata myös suorana lähetyksenä. Tapahtuma on maksuton. Ilmoittautuminen viimeistään 25.5.2022. Konferenssi järjestetään yhteistyössä The Nordic Trial Alliance, Business Finlandin ja Åbo Akademin kanssa Euroopan lääketeollisuuden ja järjestöjen liiton (EFPIA) tuella. Ilmoittautuminen, ohjelma ja lisätietoa Business Finlandin sivuilla: https://www.businessfinland.fi/en/whats-new/events/2022/future-clinical-tri… Yst. terveisin, Katja Riipinen Katja Riipinen Tutkimuskoordinaattori, FT, TtK Medical Research Center Oulu<https://www.oulu.fi/en/mrc> | MRC Oulu Oulun yliopistollinen sairaala, Oulun yliopisto OYS, Tutkimuspalvelut, N5 132 Puh. 08 315 4680, 050 448 4955 [cid:image001.jpg@01D85659.4FB66060]

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Call for applications: Cancer Partnering Day on 5 October 2022
by Johanna Kallio 22 Apr '22

22 Apr '22

Dear cancer researchers Business Finland organizes a Cancer Partnering Day - partnering & matchmaking event on 5 October 2022. The call for applications is now open for Finnish companies, health care providers, universities and research organizations, and other organizations that have products, services, or innovations relevant to the fields of interest of the attending 11 global pharma companies<https://www.businessfinland.fi/497d80/globalassets/health/interest-areas-of…>. The attending pharma companies are AbbVie, AstraZeneca, Bristol Myers Squibb, Janssen, Pharmaceutical Companies of Johnson & Johnson, Merck KGaA, MSD, Novartis, Orion, Pfizer, Roche, and Takeda. The event will be arranged in a fully digital format, which is a convenient way to begin conversations regarding potential collaborations and partnerships without the need for travel. Please apply to the event by 8 May 2022. The number of selected participants for pitches and 1-to-1 meetings is limited. The decision-makers from the 11 global pharma companies and their experts will make these selections based on the applications received. You can find more information and application instructions here: https://www.businessfinland.fi/en/whats-new/events/2022/call-for-applicatio… Br, Johanna ------------------------------------------------------------------------- Johanna Kallio, D.Sc. (Tech) Tutkimusrahoitusasiantuntija | Research funding specialist Oulun yliopisto | University of Oulu Tel. +358 29 448 5414 Mobile +358 50 479 2506 Email johanna.kallio[at]oulu.fi

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Crc April 2022