Torkel Hafting

• Lepperød, Mikkel Elle; Dragly, Svenn-Arne; Buccino, Alessio Paolo; Mobarhan, Milad; Malthe-Sørenssen, Anders; Hafting, Torkel & Fyhn, Marianne (2020). Experimental Pipeline (Expipe): A Lightweight Data Management Platform to Simplify the Steps From Experiment to Data Analysis. Frontiers in Neuroinformatics.  ISSN 1662-5196.  14 . doi: 10.3389/fninf.2020.00030 Show summary

  As experimental neuroscience is moving toward more integrative approaches, with a variety of acquisition techniques covering multiple spatiotemporal scales, data management is becoming increasingly challenging for neuroscience laboratories. Often, datasets are too large to practically be stored on a laptop or a workstation. The ability to query metadata collections without retrieving complete datasets is therefore critical to efficiently perform new analyses and explore the data. At the same time, new experimental paradigms lead to constantly changing specifications for the metadata to be stored. Despite this, there is currently a serious lack of agile software tools for data management in neuroscience laboratories. To meet this need, we have developed Expipe, a lightweight data management framework that simplifies the steps from experiment to data analysis. Expipe provides the functionality to store and organize experimental data and metadata for easy retrieval in exploration and analysis throughout the experimental pipeline. It is flexible in terms of defining the metadata to store and aims to solve the storage and retrieval challenges of data/metadata due to ever changing experimental pipelines. Due to its simplicity and lightweight design, we envision Expipe as an easy-to-use data management solution for experimental laboratories, that can improve provenance, reproducibility, and sharing of scientific projects.

• Christensen, Ane Charlotte; Lepperød, Mikkel; Lensjø, Kristian Kinden; Dragly, Svenn-Arne; Blackstad, Jan Sigurd Beddari; Fyhn, Marianne & Hafting, Torkel (2019). Perineuronal nets stabilize the grid cell network. bioRxiv - the preprint server for biology. . doi: 10.1101/796342
• Raheel, Tayyaba Qureshi; Sørensen, Christina; Berghuis, Paul; Jensen, Vidar; Dobszay, Marton B.; Farkas, Tamás; Dalen, Knut Tomas; Guo, Caiying; Hassel, Bjørnar; Utheim, Tor Paaske; Hvalby, Øyvind Christian; Hafting, Torkel; Harkany, Tibor; Fyhn, Marianne & Chaudhry, Farrukh Abbas (2019). The glutamine transporter Slc38a1 regulates GABAergic neurotransmission and synaptic plasticity. Cerebral Cortex.  ISSN 1047-3211.  29(12), s 5166- 5179 . doi: 10.1093/cercor/bhz055 Full text in Research Archive.
• Buccino, Alessio Paolo; Lepperød, Mikkel Elle; Dragly, Svenn-Arne; Häfliger, Philipp; Fyhn, Marianne & Hafting, Torkel (2018). Open source modules for tracking animal behavior and closed-loop stimulation based on Open Ephys and Bonsai. Journal of Neural Engineering.  ISSN 1741-2560.  15, s 1- 12 . doi: 10.1088/1741-2552/aacf45 Full text in Research Archive.
• Dragly, Svenn-Arne; Mobarhan, Milad; Lepperød, Mikkel Elle; Tennøe, Simen; Fyhn, Marianne; Hafting, Torkel & Malthe-Sørenssen, Anders (2018). Experimental directory structure (Exdir): An alternative to HDF5 without introducing a new file format. Frontiers in Neuroinformatics.  ISSN 1662-5196.  12 . doi: 10.3389/fninf.2018.00016
• Mobarhan, Milad; Halnes, Geir; Martínez-Cañada, Pablo; Hafting, Torkel; Fyhn, Marianne & Einevoll, Gaute (2018). Firing-rate based network modeling of the dLGN circuit: Effects of cortical feedback on spatiotemporal response properties of relay cells. PLoS Computational Biology.  ISSN 1553-734X.  14(5) . doi: 10.1371/journal.pcbi.1006156 Full text in Research Archive.
• Rowlands, Daire; Lensjø, Kristian Kinden; Dinh, Tovy; Yang, Sujeon; Andrews, Melissa; Hafting, Torkel; Fyhn, Marianne; Fawcett, James W. & Dick, Gunnar (2018). Aggrecan directs extracellular matrix mediated neuronal plasticity. Journal of Neuroscience.  ISSN 0270-6474.  38(47), s 10102- 10113 . doi: 10.1523/JNEUROSCI.1122-18.2018 Show summary

  In the adult brain, the extracellular matrix (ECM) influences recovery after injury, susceptibility to mental disorders, and is in general a strong regulator of neuronal plasticity. The proteoglycan aggrecan is a core component of the condensed ECM structures termed perineuronal nets (PNNs), and the specific role of PNNs on neural plasticity remains elusive. Here, we genetically targeted the Acan gene encoding for aggrecan utilizing a novel animal model. This allowed for conditional and targeted loss of aggrecan in vivo, which ablated the PNN structure and caused a shift in the population of parvalbumin expressing inhibitory interneurons towards a high plasticity state. Selective deletion of the Acan gene in the visual cortex of male adult mice reinstated juvenile ocular dominance plasticity, which was mechanistically identical to critical period plasticity. Brain-wide targeting improved object recognition memory.

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• Hagen, Espen; Stasik, Alexander Johannes; Billeh, Yazan N.; Siegle, Joshua H.; Dai, Kael; Rimehaug, Atle Eskeland; Ness, Torbjørn V; Røe, Malin Benum; Fyhn, Marianne; Hafting, Torkel; Koch, Christof; Olsen, Shawn R.; Einevoll, Gaute & Arkhipov, Anton (2019). Comparing spikes and the local field potential (LFP) in V1 between experimental data and a comprehensive biophysical model.
• Hagen, Espen; Stasik, Alexander Johannes; Billeh, Yazan; Siegle, Joshua H.; Dai, Kael; Rimehaug, Atle Eskeland; Ness, Torbjørn V; Røe, Malin Benum; Fyhn, Marianne; Hafting, Torkel; Koch, Christof; Olsen, Shawn R.; Einevoll, Gaute & Arkhipov, Anton (2019). Comparing spikes and the local field potential (LFP) in V1 between experimental data and a comprehensive biophysical model.
• Røe, Malin Benum; Aasebø, Ida Elisabeth Jørgensen; Mobarhan, Milad; Lensjø, Kristian Kinden; Einevoll, Gaute; Hafting, Torkel & Fyhn, Marianne (2019). Stable orientation tuning in the freely moving rat: Movement-robust orientation-selective neurons in the deep layers of the primary visual cortex.
• Røe, Malin Benum; Aasebø, Ida Elisabeth Jørgensen; Mobarhan, Milad; Lensjø, Kristian Kinden; Einevoll, Gaute; Hafting, Torkel & Fyhn, Marianne (2019). Stable orientation tuning in the freely moving rat: Movement-robust orientation-selective neurons in the deep layers of the primary visual cortex.
• Aasebø, Ida Elisabeth Jørgensen; Fyhn, Marianne; Hafting, Torkel & Einevoll, Gaute (2018). Behavioural state and neuronal activity: how the freely moving paradigm can uncover novel response characteristics..
• Aasebø, Ida Elisabeth Jørgensen; Røe, Malin Benum; Mobarhan, Milad; Lensjø, Kristian Kinden; Stöber, Tristan Manfred; Einevoll, Gaute; Hafting, Torkel & Fyhn, Marianne (2018). Orientation selectivity in the freely moving rat: Movement-robust orientation-selectivity (MROS) of units in the deep layers of the rat visual cortex.
• Dragly, Svenn-Arne; Mobarhan, Milad; Lepperød, Mikkel Elle; Tennøe, Simen; Stasik, Alexander Johannes; Fyhn, Marianne; Hafting, Torkel & Malthe-Sørenssen, Anders (2018). Exdir An alternative to HDF5 that uses Numpy files for data, YAML for metadata and simple directories to define the hierarchy.
• Grødem, Sverre; Sandvik, Guro Katrine; Hazen, Jennifer; Lensjø, Kristian Kinden; Hafting, Torkel & Fyhn, Marianne (2018). A CRISPR-Cas9 platform for genetic perturbations of brain extracellular matrix regulators in vivo.
• Hafting, Torkel (2018). Brain plasticity an perineuronal nets.
• Hafting, Torkel (2018). Brain plasticity, perineuronal nets and long-term memories.
• Hazen, Jennifer; Wigestrand, Mattis B; Aasebø, Ida Elisabeth Jørgensen; Tully, Annabelle; Dinh, Tovy; Lepperød, Mikkel; Hafting, Torkel & Fyhn, Marianne (2018). Lateral hypothalamic area projection neurons contribute to an innate freezing response.
• Lensjø, Kristian Kinden; Rowlands, Daire; Dinh, Tovy; Thompson, Elise Holter; Andrews, Melissa; Hafting, Torkel; Fawcett, James; Dick, Gunnar & Fyhn, Marianne (2018). Conditional knock-out of the Acan gene removes perineuronal nets in adult mice and induces life-long brian plasticity.
• Røe, Malin Benum; Aasebø, Ida Elisabeth Jørgensen; Mobarhan, Milad; Lensjø, Kristian Kinden; Einevoll, Gaute; Hafting, Torkel & Fyhn, Marianne (2018). Movement-resistant orientation selectivity of cells in the deep layers of the rat visual cortex.

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