NIN Self-Evaluation

Self-evaluation document for the site visit of the Netherlands Institute for Neuroscience

“We strive to uncover the brain circuits necessary to adapt to a changing world”

2012 - 2017

Table of Contents Mission statement ...... 1 The institute’s position and strategy ...... 1 Research quality ...... 5 Relevance to society ...... 6 Financial situation and fund-raising ...... 6 Organization ...... 7 Collaborations within the institute ...... 9 The institute’s hub function within the Netherlands ...... 9 Facilities ...... 10 Teaching of PhD students ...... 11 Research Integrity ...... 12 Diversity ...... 13 Housing of the NIN ...... 13 SWOT: Analysis ...... 14 Appendix 1 Organogram 2018 and Scientific Advisory Board Appendix 2 Research output Appendix 3 Funding situation Appendix 4 Research staff Appendix 5 Narrative on societal impact Appendix 6 Results of the bibliometric analysis Appendix 7 Success of PhD training Appendix 8 Future housing scenarios Appendix 9 Honors, prizes and awards Appendix 10 Information about the research groups Appendix 11 The Netherlands Brain Bank Appendix 12 The conclusion and recommendations of the previous peer review Appendix 13 Response of the board of KNAW to the previous assessment report Appendix 14 The most recent mid-term assessment

This document describes the research program of the Netherlands Institute for Neuroscience (NIN) and our plans for the future. The research and achievements of the individual research groups are outlined in Appendix 10.

Mission statement The NIN aims to explain how circuits of neurons enable us to see the world and act upon it.

The institute’s position and strategy We aim to understand how circuits of neurons enable brain functions. The research of the institute bridges the neuroscience of nerve cell function, the functioning of circuits of neurons and the functioning of the brain at a psychological level of description. NIN researchers implement many new tools to investigate the interactions between neurons, adopt methods to influence neuronal activity and investigate the consequences The institute is an important nexus in the of these interventions for behavior. Netherlands for fundamental research into Examples of brain functions that we study circuits of nerve cells. include, but are not limited to, visual perception, attention, memory, motor behavior, sleep and empathy. The institute is an important nexus in the Netherlands when it comes to fundamental research into circuits of neurons. This position is based on the composition of the expert research groups and on the state-of-the art facilities and equipment to study the circuits in the brain. Many of the NIN researchers are young and they fan out to other research organizations to apply the knowledge that they acquired at the institute. Scope of scientific field The strategy of the institute is to host excellent research groups that span the continuum of topics from vision (starting in the retina) all the way to the system’s output (action), where output should be considered in its most encompassing meaning, including sleep, eating, and the endocrine system. At the same time, researchers at the institute cover a continuum of levels of investigation, ranging from the molecular level to the social level of brain-to-brain analyses. Many of the groups use in silico simulations to interpret their data and generate new, testable hypotheses. To generate critical mass, and to enable investment in advanced techniques, the institute has recruited groups that overlap in topic and level of investigation. The resulting synergies have created an exciting environment that enables groups to collaborate, exchange expertise and share equipment (Figure 1).

1 A

Figure 1: (A) Research groups at the NIN. Structural groups receive the bulk of their financial support from the NIN, and honorary groups are funded by other organizations. (B) Number of research groups studying the topics (x-axis) ranging from vision to action at the levels (y-axis) from molecules to brain-to-brain analysis. The line-plots at the top and side represent the number of groups investigating that topic (top) or level (side) at any level (top) or topic (side). The long-term investment in expertise and facilities for research into circuit function makes the institute FUNDAMENTAL unique in the Netherlands and complements research carried out at Dutch universities. There is an intensive RESEARCH collaboration with the universities. This is reflected, in part, by the 15 chairs at Dutch universities and Research into the academic medical centers held by influential NIN functioning of healthy research group leaders (Box 1). The NIN attracts and brains and brain diseases trains a new generation of researchers, including is a long-term investment young principal investigators (PIs), postdocs and PhD of great societal students. With regard to young PIs, Dutch universities have attracted a number of researchers who first built importance. Brain diseases their own group at the NIN. For example, the are a large health care universities of Utrecht and Leiden, and the AMC burden, costing over 800 (Academic Medical Center of the University of billion euros per year in Amsterdam) recruited Elly Hol, Jan Wijnholds and Europe, and expected to Arthur Bergen, respectively (2013-2014). rise due to the aging of Furthermore, the VUmc recruited Ysbrand Van der the population. Continued Werf in 2015 and the University of Amsterdam appointed Helmut Kessels as full professor in 2018. investments in fundamental brain Within the Netherlands, the academic medical centers research are crucial focus on translational and patient-related research because fundamental with the aim of improving treatments for the short and medium term. Research at the NIN is complementary insights and techniques to that, with its focus on fundamental new insights most often inspire new into brain function. It thereby helps to safeguard therapies. fundamental research in the Netherlands, which has been under increasing financial pressure 1 . To facilitate the translation of innovative treatments in the longer term, NIN researchers collaborate with several medical centers, including the AMC, VUmc, Leiden University and the Erasmus University Rotterdam. These collaborations are structured through mutual appointments and honorary group- leaderships of PIs of medical centers at the institute (Box 1). The institute makes its research climate attractive by bringing together top researchers in a flat organization, where PIs have a say in the important decisions, and are given first- class facilities and resources. For research on the human brain, the institute founded the renowned Netherlands Brain Bank and it is one of the founders of the Spinoza Centre for Neuroimaging, providing researchers access to 3T and 7T MRI scanning facilities.

1 https://www.knaw.nl/shared/resources/actueel/publicaties/pdf/binnenwerk-advies-witte-vlekken-ruimte-voor- ongebonden-onderzoek

2 Box 1: Chairs at universities and academic medical centers

Damiaan Denys AMC-UvA Birte Forstmann UvA & Leiden University Andries Kalsbeek AMC-UvA Maarten Kamermans AMC-UvA Christian Keysers UvA Maarten Kole University of Utrecht Susanne la Fleur AMC-UvA Christiaan Levelt VU Christian Lohmann VU Pieter Roelfsema AMC-UvA & VU Joost Verhaagen VU Eus van Someren VU Dick Swaab Zhejiang University Hangzhou, China Chris de Zeeuw Erasmus University Rotterdam Moreover, the institute has a well-equipped sleep lab and the Dutch Sleep Register. Furthermore, there is unique expertise in single-cell recordings in patients implanted with depth electrodes as part of their epilepsy treatment. Fundamental brain research requires animal models. The NIN has facilities for research with rhesus monkeys, rats, mice and zebrafish. To register the activity of circuits of neurons during behavior, the institute has 2-photon microscopes, electrophysiological setups and facilities for chemo- and optogenetics. Noteworthy is that the NIN took the lead in Europe in the development of ultralight miniature microscopes to measure the activity of cells in multiple brain areas. These facilities for fundamental research are greatly valued by our academic partners. Specifically, the institute forms essential links between clinical and cellular research at the AMC, the VU University Amsterdam (VU) and the University of Amsterdam (UvA - Swammerdam Institute for Life Sciences and the Amsterdam Brain and Cognition Center, ABC). Targets for the period 2012-2017 Before 2012, the institute attracted young research talent to increase the dynamics of its overall portfolio. Because the research themes were deemed too broad in 2012, one of the main goals for 2012-2017 was to narrow the focus of the institute's activities to the groups that were central to its mission. An important additional goal The research groups present in the institute was to balance the expenses with the overall budget available to the enable a coherent research program and institute. Both goals were achieved inspire collaborations between the groups. when the institute facilitated the transition to various universities of three groups with research topics that were much better suited to the research programs of these universities. The remaining research groups enable a coherent research program and inspire collaborations between the groups. Many of the groups use methods to monitor the activity of neurons in different brain structures and the institute has invested substantially in methods for the imaging and electrophysiology of large groups of neurons. The philosophy of the NIN is to invest in lean groups. Although the productivity of research groups increases with their size, the slope is shallow. Hence, the institute divides the funding as a lump sum across a number of lean research groups, averaging 5.5 scientists each. We have also introduced a 10% overhead on grants. These measures, together with the reduction of the total number of research groups, have led to a healthy financial long- term situation. The opening of the Spinoza Centre for Neuroimaging in 2015 meant an important boost for the NIN's research program, because the research of a number of its groups relies on access to MRI facilities for humans and non-human primates. The Spinoza Centre is a collaboration between the University of Amsterdam, the Vrije Universiteit Amsterdam, the AMC and the Royal Netherlands Academy of Arts and Sciences (KNAW). The way in which this center will continue after 2019 is now being discussed by the partners.

3 Research quality Relevance to society Products • Research articles • Books for a general audience • Research articles IF> 9 • Articles in journals for non- • Scientific/scholarly books academic readers • Dissertations • Media engagement and lectures for general audiences • Products for research and new treatments at the longer term Use of • Citations • Patents/licenses products • Use of tissue of the Netherlands Brain Bank • Media appearances • Sleep registry Marks of • Science awards/ scholarly prizes • Valorization funding recognition • Research grants awarded to • Membership civil society individuals advisory bodies Table 1: Output indicators of the NIN. Continuation of the center is crucial for the research program of the NIN. Indeed, the presence of the Spinoza Centre has been highly beneficial in terms of the acquisition of grants. Specifically, ~M€ 11 in NIN funding was acquired in part by the possibility to perform 3T and 7T scanning. One aim that we set for 2012-2017 but that has not yet been achieved is to improve the housing situation for the institute. The previous peer-review committee also recommended that we increase the use of the non-human primate facility, because research with rhesus monkeys is essential for the understanding of higher cognitive functions and for the development of innovative therapies. The NIN is now the only institution in the Netherlands where neuroscience research with non-human primates takes place, and the institute thereby fulfills a similar role to that of the Max-Planck Institutes in Germany. In 2014, the KNAW issued a report indicating that non-human primate brain research is and will continue to be essential for a number of important scientific questions. The same conclusion was reached at the European level in the 2017 SCHEER (Scientific Committee on Health, Environmental and Emerging Risks) report to the European Commission. Strategy for the period 2018-2023 Some of the targets for the coming period are the logical consequence of unfulfilled aims of the previous period. First, we aim to work together with the KNAW to improve the housing situation of the GOALS institute. Furthermore, we will facilitate the continuation of the Spinoza Centre for Neuroimaging after 2019. One of the goals of the One of the goals of the institute is to be a place that trains institute is to be a place that the next generation of leaders in the field of trains the next generation neuroscience, and to provide the core facilities for their of leaders in the field of research and to enable them to attract grants, securing a neuroscience. continued flexibility of the research program. Another aim is to strengthen the developing techniques that are innovative and important. They permit new collaboration between the existing groups and will further strengthen the position of the institute as central neuroscience hub in the Netherlands. Further innovation of the research program is possible because of the retirement of a number of PIs in the coming period. Furthermore, the transition of Helmut Kessels to the University of Amsterdam will allow us to attract a new research group to the institute. This vacancy will provide us with the opportunity to further increase the gender diversity. The research program of the NIN fits squarely in the National Research Agenda, which will guide substantial national research investments in the Netherlands in the coming years. The research of the NIN will contribute to a number of tracks of the National Research Agenda, including the “NeuroLabNL” route, which aims to achieve scientific breakthroughs in our understanding in brain function. The research will also contribute to the national “Top Sector” policy, facilitating the translation of scientific insight into new products. The NIN coordinates the consortium “NeuroTech-NL” within the Top Sectors “Life Science and Health” and “High Tech Systems and Materials”.

4 Box 2: Top papers 2012 - 2017

Gazzola V, Spezio ML, Etzel JA, Castelli F, Adolphs R, Keysers C. (2012) Primary somatosensory cortex discriminates affective significance in social touch. Proc Natl Acad Sci U S A 109: E1657-1666.

Ahmadlou M, Heimel JA (2015) Preference for concentric orientations in the mouse superior colliculus. Nat Commun 2: 6773.

Cerliani L, Mennes M, Thomas RM, Di Martino A, Thioux M, Keysers C (2015) Increased functional connectivity between subcortical and cortical resting-state networks in autism spectrum disorder. JAMA Psychiatry 72: 767-777.

Lorteije JAM, Zylberberg A, Ouellette BG, De Zeeuw CI, Sigman M, Roelfsema PR (2015) The formation of hierarchical decisions in the visual cortex. Neuron 87: 1344–1356

Winnubst J, Cheyne JE, Niculescu D, Lohmann C (2015) Spontaneous activity drives local synaptic plasticity in vivo. Neuron 87: 399-410.

Battefeld A, Klooster J, Kole MHP (2016) Myelinating satellite oligodendrocytes are integrated in a glial syncytium constraining neuronal high-frequency activity. Nat Commun 7: 11298.

Gutierrez-Castellanos N, Da Silva-Matos CM, Zhou K, Canto CB, Renner MC, Koene LM, Ozyildirim O, Sprengel R, Kessels HW, De Zeeuw CI. (2017) Motor learning requires Purkinje cell synaptic potentiation through activation of AMPA-receptor subunit GluA3. Neuron 18: 409-424.

Hammerschlag AR, Stringer S, de Leeuw CA, Sniekers S, Taskesen E, Watanabe K, Blanken TF, Dekker K, Te Lindert BHW, Wassing R, Jonsdottir I, Thorleifsson G, Stefansson H, Gislason T, Berger K, Schormair B, Wellmann J, Winkelmann J, Stefansson K, Oexle K, Van Someren EJW, Posthuma D (2017) Genome-wide association analysis of insomnia complaints identifies risk genes and genetic overlap with psychiatric and metabolic traits. Nat Genet 49: 1584-1592.

Klink PC, Dagnino B, Gariel-Mathis MA, Roelfsema PR (2017) Distinct feedforward and feedback effects of microstimulation in visual cortex reveal neural mechanisms of texture-segregation. Neuron 95: 209- 220.

Sommeijer JP, Ahmadlou M, Saiepour MH, Seignette K, Min R, Heimel JA, Levelt CN (2017). Thalamic inhibition regulates critical-period plasticity in visual cortex and thalamus. Nat Neurosci 20: 1715-1721. This consortium aims to generate new invasive brain devices for patients, including a visual prosthesis for the blind and novel applications of deep brain stimulation technology.

Research quality As an institute for fundamental research, the important indicators of output are the number of publications, their impact, citation scores and the ability of group leaders to attract external funding (Table 1). The quality and stature of the NIN is evident from the impact of the NIN-publications, many of which are in high-ranking journals (Figure 2, Appendix 2 and Box 2). The NIN is internationally visible as an excellent brain research institute. Other indications of its visibility are the ability to attract talented PIs and the wide range of collaborations with research groups around the world (Appendix 10). The institute is international in its make-up, with employees from at least 27 nationalities. Overall, the NIN is an institute with a relatively young staff that implements an innovative research program. The output of the institute is high and of considerable impact, and it is expected that the institute’s international position will be further enhanced in the coming years, as a natural consequence of the staff’s maturation.

Figure 2: Research output-articles. The bar shows the average number of publications per year in the period 2012-2017 and the previous 6-year period. The red bar shows the average number of publications per year in journals with an impact factor (IF) above nine.

Scientific output Researchers at the NIN published on average 179 papers per year in the period between 2012 and 2017 (Figure 2, Appendix 2, and Box 2). The productivity has increased relative to the previous 6-year period and this is particularly evident when we focus on publications in higher impact journals. The number of defended PhD theses varies between 5 and 15 per year. The growth in recent years is due to an ability to attract external grants, which are often used to appoint PhD students. International benchmarking As benchmarks for the NIN, we chose a number of internationally renowned research institutes: the Janelia Research Campus (USA), the Champalimaud Center for the Unknown (Portugal), the Max-Planck Institute for Neurobiology (Germany) and the Institute for Neurosciences and Medicine (Germany) (Table 2).

5 Institute Organization City, lump sum grants total Staff Publ. Papers/Staff Country 1 Janelia Research HHMI all Ashburn, VA, 800,000 unknown unknown 530 194 0.37 Campus USA Neuro unknown unknown unknown 3402 125 0.37 Champalimaud Champalimaud Lisbon, P 6,0003 4,500 unknown 175 71 0.41 Neuroscience Foundation Programme Max-Planck Max Planck Martinsried, 14,0003 1,100 15,100 129 51 0.40 Institute of Gesellschaft D Neurobiology Institute of Jülich Jülich, D 33,0004 4,683 unknown 200 212 1.06 Neurosciences Forzungszentru and Medicine m Netherlands KNAW Amsterdam, 9,711 5,991 16,903 117 1795 1.53 Institute for NL + 1,201

Neuroscience (other) Table 2: international benchmarking (financial numbers are indicated in units of KEuro/year)

1) Scientific staff includes faculty, PIs, postdocs, scientists and PhD students 2) Estimate 3) Excl. Housing 4) Total for FZJ 5) Yearly average in 2012-2017 Unfortunately, not many of these institutes disclose information about their level of direct funding. However, it is possible to compare the number of research staff to the institute’s output. The average number of papers per member of the research staff at the NIN equals 1.53, which is substantially higher than that of the other institutes included in this benchmark. We suspect that the research output reflects the encouraging climate for fundamental research at the NIN. We have not been able to analyze the precise cause of these differences between institutes, which would also require a careful analysis of the types, impact and quality of publications of all institutes. Citation analysis The citation analysis of CWTS (Appendix 6), an independent institute specializing in citation analyses, revealed that the impact of NIN papers is nearly 1.6 times world average. This is considerably higher than the threshold at which CWTS assigns the ‘high impact’ label (1.2 times world average). Furthermore, the visibility indicator (percentage of papers in the top 10%) shows an even more pronounced pattern of ~2 times world average. We conclude that the NIN researchers are not only very productive compared to the international benchmark, but that the institute’s papers also rank far above world average on normalized impact and visibility indices.

Relevance to society Given the impact of brain disease on society, understanding the workings of the brain is of great societal relevance - for the general public, for patients and their organizations, for other researchers in fundamental neuroscience and in translational neuroscience, for the national and European government, and for the industry. In this way, we ensure that the fundamental knowledge we generate in the institute (i) inspires the public, (ii) helps influence policy, (iii) helps patients directly and indirectly via the stimulation of translational research and (iv) energizes the economy with innovative products. We provide details of our strategies to achieve these goals in the “Narrative on Societal Impact” (Appendix 5).

Financial situation and fund-raising ~55% of NIN funding is direct funding by the government, through the KNAW (this includes housing costs, energy costs etc., Appendix 3) with the remaining ~45% of support coming through grants. The amount of funding obtained through grants was at a level of approximately M€ 6 per year between 2012 and 2017, which is ~70% of the primary funding of M€ 9.7 by the KNAW. This corresponds to an average of k€ 375 per research group per year, although there are differences between the groups. Accordingly, the average number of researchers working at the institute in the period 2012-2016 was 88 fte, of which 41 were PhD students (Appendix 4).

One of the recommendations of the peer-review committee of 2012 was to increase the number of ERC grants and other prestigious grants. The group leaders were very successful in attracting prestigious personal grants, especially in the past few years. Of the 17 group leaders, seven have acquired an ERC-grant and 11 have acquired a Vidi/Vici- grant, with 11 of these grants being awarded in the period 2012-2017. In addition to these personal grants, the institute was successful in attracting program grants, including six TOP and Memorabel and ERA-NET Grants. Furthermore, the Netherlands Brain Bank is partially funded by an NWO-Groot grant. As a general rule, group leaders are asked to triple the lump sum (of k€ 139/year) they receive from the institute by acquiring external grants. They have mostly been successful in doing this (Appendix 9).

Organization The NIN is one of the larger institutes of the KNAW. The institute is led by a board of three directors (see Appendix 1 for the organizational chart). The two scientific directors are Pieter Roelfsema (general director) and Chris De Zeeuw (vice director) whose combined expertise covers the disciplines represented at the institute, from molecular neuroscience up to cognition. As general director, Pieter Roelfsema reports to Mieke Zaanen, LL.M., the director general of the KNAW. He also participates in the KNAW directors’ meeting of the 15 institutes of the KNAW. Ronald Van der Neut is managing director and is responsible for the support staff. The board of directors takes the strategic decisions for the institute The NIN has a flat organization geared and meets twice a month. In addition to the towards stimulating high quality, 17 PIs and their research groups, the institute fundamental neuroscience research. employs research support staff and personnel for the finance department, human resource management and other administrative services. The total number of full time positions at the institute is 160 (fte; the actual number of employees is ~175). The NIN has a flat organization geared towards stimulating high quality, fundamental neuroscience research. All PIs are independent and only report to the directors. They are responsible for managing the lump sum allocated to their group, along with the external grant funds they obtain. The PIs have limited teaching obligations and are expected to be strongly involved in the research projects of all group members. The PIs directly supervise their PhD students and postdocs, ensuring high quality training of young scientists. The PIs work on research subjects that are directly related to the main research theme of the institute - neural circuits in perception and action - but use different state-of-the-art experimental approaches. This stimulates collaboration between the groups and lowers the threshold for using novel experimental approaches to pursue important research questions. The PIs can aspire to excel in neuroscience research and are or aim to become leaders in their fields at the national and European level as well as being highly visible on a global level (Appendix 10).

7 Figure 3: Collaborations. Left, collaborations within the institute. The type of collaboration, joint grant/publication, joint project (plan) has been color-coded. Right, collaborations of the NIN with Dutch academic and academic medical centers. Line thickness is proportional to the total number of formal affiliations, papers published and grants awarded in the last five years. Smallest line width corresponds to 1, largest width to 28. RUG, University of Groningen; UvA, University of Amsterdam; VU, VU University Amsterdam; LU, University of Leiden; EUR, Erasmus University Rotterdam; UU, University of Utrecht; UT, technical University Twente; RUN, Radboud University Nijmegen; TU, University of Tilburg; TUe, technical University Eindhoven; UM, University of Maastricht. There are two types of research groups: Structural groups (11), which receive comparable (and substantial) financial support (k€ 139/year + PI salary) and honorary groups (6), which also have a research group in another organization and receive limited support from the NIN, tailored to the unique composition and situation of each group. The honorary research groups are selected based on mutual benefit for both parties. The honorary groups make use of NIN facilities and provide technical and scientific expertise to the institute. Finally, the NIN provides high quality research facilities. There is support staff to assist scientists with financial administration, human resource management, IT facilities, general lab facilities, the animal facilities, a mechatronics department (support for mechanical and electronical projects), secretarial support and communication. The heads of the support staff have a meeting with the managing director every 6 weeks. Once a month, group leaders and board of directors discuss scientific and organizational issues during the group leader meeting. The institute has an external scientific advisory board, which is chaired by Simon Fisher and meets on average once per year. In addition to the scientific lectures, PhD students and postdocs have their own representatives, who organize meetings about matters of organization. The PhD and postdoc representatives join the board meetings 1-2 times per year and the board also has annual plenary meetings with the PhD students and with the postdocs. The works council (OC), representing all employees of the NIN, has meetings with the board six times per year. The research program is dynamic. Since 2007, the institute has attracted 15 new groups, seven of which joined in the period 2012-2017. The NIN’s dynamic and flexible nature provides young PIs with the opportunity to start their independent research lines. In the past, groups left the institute to continue their research at various universities, after a successful period at the NIN. The institute thereby complements the university system in an important manner. Scientific discussion The coherent research program of the NIN has created innovative research lines as the result of interactions between the groups. To facilitate these scientific interactions, the institute organizes meetings about the research questions and results. There is a weekly neuroscience symposium, where groups present their latest findings. Furthermore, at every group leader meeting, one of the PIs gives a presentation about a new finding, method or technique that could be of interest to the other PIs. There are also internal research meetings and journal clubs within groups or jointly with one or two other groups. Brain Prizes To honor important contributions of the PhD students and postdocs, the NIN launched the “Brain Awards”. There are separate Brain Awards PhD students and postdocs in three categories: scientific excellence, methodological excellence and collaborative excellence (promoting collaborations between research groups).

8 Box 3: Collaboration within the NIN - Emotional Mirror Neurons.

At the NIN, the group of Christian Keysers has evolved from a typical human fMRI research group into a multidisciplinary one, combining many different approaches. The group originated in Groningen, where, with the use of fMRI studies, it established that humans recruit brain regions involved in their own emotions while witnessing the emotions of others. These experiments opened a new avenue of research, which could not be capitalized on, as application of fMRI technology alone was unable to answer emerging key questions such as (i) are the same neurons involved in emotion experience and observation, (ii) are these neurons selective for specific emotions, and (iii) would altering the activity in these neurons alter empathy and prosociality? To answer these questions the next step was to develop and test a rodent model for empathy, for which the NIN offered the ideal environment. After moving to the NIN, the group started to collaborate with Christiaan Levelt (molecular techniques), Chris De Zeeuw (electrophysiology, and multi-photon microscopy), and Ingo Willuhn (GECO in rats). The collaborative culture at the NIN, and the intellectual curiosity shared as a core value meant that these groups’ expertise in rodent neuroscience guided Christian Keysers in vesting his social neuroscience questions in strong, cutting edge yet feasible rodent neuroscience experiments. The rich equipment base at the NIN then allowed Christian’s research group to efficiently and quickly generate proof-of-concept data that these approaches can work at the NIN and that empathy can be studied at the neural level in rodents. These pilot data, as well as the strong embedding, allowed obtaining several ERC, NWO (Vidi, Vici) and Marie Curie grants and meant the start of a bold refocusing of the research lines towards a trans-species approach that is starting to unlock the cellular mechanisms of empathy.

Figure I: Single cell recordings using silicon probes in the rodent ACC (a) in regions equivalent to the human regions associated with empathy for pain (b) responses to both the observation (c) and experience (d) of shocks. These data could be acquired through intense collaborations within the institute. Collaborations within the institute The groups have complementary expertise and shared interests. This, in combination with the open and collaborative atmosphere and the common goal to understand the circuitry of the brain, has fostered a large number of collaborations (Figure 3, Box 3). Many of these have resulted in joint publications and awarded grants. Other collaborations are technical (e.g. sharing animal lines, viral vectors, experimental setups or computing power). Although this type of collaboration does not always yield co-authorships, it does contribute to making the institute an ideal place for researchers to explore questions beyond their own level of expertise and allowing them to venture into new areas and technologies.

The institute’s hub function within the Netherlands The institute has collaborations with most Dutch universities and academic medical centers (Figure 3). The NIN has particularly strong collaborations with the two universities in Amsterdam. The first is the University of Amsterdam (UvA) and its academic medical hospital (AMC), on whose campus the NIN is housed. The second university is the VU University and its hospital (VUmc), located at a distance of 10 km. The close collaboration between the UvA, the VU and the NIN-KNAW has resulted in the Spinoza Centre for Neuroimaging (Box 4). The NIN’s research lines with links to diseases benefit from the interaction with the academic hospitals. Some of the collaborations with the AMC are structured through mutual appointments of NIN researchers at the AMC and vice versa. Andries Kalsbeek, Ingo Willuhn/Damiaan Denys and Susanne La Fleur combine appointments at the AMC with an honorary group at the NIN. In addition, Maarten Kamermans and Pieter Roelfsema have chairs at the AMC. The NIN also has strong links with the neuroscience department at the VU University’s Neuroscience Campus. A number of these collaborations (Eus van Someren, Christiaan Levelt, Christian Lohmann, Joost Verhaagen and Pieter Roelfsema) are formalized through chairs. Birte Forstmann has a chair at the psychology department at the UvA and an honorary group at the NIN. Christian Keysers also has a chair in the psychology department of the UvA, Maarten Kole has a chair at the University of Utrecht and Chris De Zeeuw has a chair in Rotterdam (Box 1). As the main KNAW neuroscience institute, the NIN is a center of expertise at the national level with collaborations with neuroscience departments of other universities, also outside Amsterdam. We have strategic alliances with the ErasmusMC in Rotterdam, Utrecht University and the University of Leiden, and we collaborate with researchers at most of the other universities (Figure 3). Many of our scientific collaborations include partners outside the Netherlands, often structured through EU-grants and grants of other funding organizations. A number of our facilities, such as the Netherlands Brain Bank and the non-human primate facility are essential parts of the national research structure and contribute to multiple national research programs.

9 Box 4: Collaborations among KNAW-organizations NIN, NBB and Spinoza Centre: in vivo and post-mortem imaging.

The Spinoza Centre for neuroimaging (SC), adjacent to the NIN, opened its doors in 2015. The short- distance conglomerate of NIN, SC and NBB has generated new fascinating opportunities for both in vivo and post-mortem imaging. Together, this has allowed groups at the NIN to obtain over 11M€ in grants for projects where innovative neuroimaging plays a critical role. The groups of Forstmann, Gazzola, Keysers, Roelfsema and Van Someren carry out in vivo imaging in humans. In particular, the availability of 7T MRI has been crucial for projects looking at layer-specific activity (Keysers), at fine- grained anatomical details (Forstmann) or for designs in which a small number of trials can be acquired (Gazzola). Having 3T MRI available next door is particularly important for non-human primate studies and allows the group of Roelfsema to precisely functionally identify vision-relevant domains in various parts of the occipital, parietal and frontal lobe of the cerebral cortex. They subsequently use electrophysiological recordings at the NIN to find the neural correlates of the same functional domains at the single cell level. Likewise, the SC and NBB have set up a pipeline to facilitate 3T and 7T in situ post-mortem imaging of brains, to bridge the current gap between the µm scale of histology of human brain tissue and the mm scale resolution of MRI brain scans. In particular, post- mortem imaging will identify the histo(patho)logical, cellular and molecular correlates of MRI signals, help to optimize the MRI sequences that enable detection of specific histological features and molecular and cellular changes of interest in vivo, allow precise MRI-guided dissection of functional regions for proteomic, genomic and histological mapping of brain functions, and facilitate MRI-guided dissection of pathologies invisible to the naked eye. Researchers can apply at NBB/SC for 3T and 7T in situ scans of control donors and donors with neurological or psychiatric diseases and tissue of choice for further analysis. One major technical issue when attempting to bring histology and MRI together is that post-mortem delays and fixation very strongly affect the MRI signal, making the comparison of MRI in living (in vivo) and extracted brain tissue (ex vivo) challenging. The 24/7 availability of both the SC and the NBB allows scanning post-mortem brains at ultra-high field MRI in situ, prior to fixation, with extremely short post-mortem times, of between 2 and 6h.

Figure II: Measuring the human brain at different spatial scales (factor of 1000). The white lines in the different panels represent 0.035 to 10 millimeter (mm) lengths. (A) Preliminary results (a 2D stack of 20 mm optical sections) on CLARITY-cleared human tissue from 10-15 mm tissue blocks stained for three different interneuron types. (B) The cleared tissue blocks. (C) Individual microglial staining. (D) MRI scan of the human brain. Finally, the institute develops new methods and techniques (e.g. Box 5) and makes them available to other researchers in the Netherlands.

Facilities Netherlands Brain Bank (NBB): The NBB collects postmortem human brain tissue of donors with neurological and psychiatric disorders, as well as of healthy donors. Brain tissue plus an anonymized summary of the medical record of the subject involved is supplied to scientists worldwide (Appendix 11). The director of the NBB is Inge Huitinga. Since 2012, an average of 117 brain autopsies have been performed per year, and every year over 5,000 tissue samples have been supplied to institutes in 47 countries across the globe. This has resulted in more than 500 publications since 2012 (90 in journals with IF > 8; 36% from NIN researchers). In 2012, in collaboration with several academic medical centers and universities in the Netherlands, the NBB acquired an NWO-Groot grant, which will continue until at least 2022. Primate Brain Bank: This bank collects and distributes brain material of 46 species of primates (300 specimens), including apes (gorilla, chimpanzee, orangutan, gibbon) to researchers. The origin of the material is ethically sound (e.g. from zoos). Pieter Roelfsema is coordinator of the Primate Brain Bank. Animal facility: In addition to a transgenic unit (5,000 mice, ~170 transgenic lines), an experimental rodent unit (2,000 mice and 500 rats), a DM-II unit for viral vector applications (150 mice and 75 rats), and a Zebra fish unit (7,000 fish, 15 transgenic lines), this facility houses a macaque unit (20 primates), the only non-human primate facility for cognitive neuroscience in the Netherlands. Gerrit-Jan Wennink DVM is the head of the animal facility. Sleep lab: The institute has a human sleep laboratory with four insulated bedrooms enabling manipulation of sleep while monitoring the participants’ performance and recording their high-density EEG (256 channels). The lab is supervised by Eus Van Someren. Many participants are recruited through the Netherlands Sleep Registry, which is also coordinated by the NIN. Motion lab: The motion lab houses a combined hexapod turntable and 3-D projection screen that is unique in the world in that it can rotate and translate the vestibular and visual stimuli in any direction, while recording electrophysiological activity of the brain as well as the eye movements of both eyes in rodents or macaques. The lab, which is coordinated by Chris De Zeeuw, is used as a training and phenotyping center by many scientists in Europe, US and Asia. Microscopic Imaging facility: There are currently seven two-photon setups with or without virtual reality stimulation, and even more light-, epi-fluorescent and confocal microscopes. The imaging set-ups are looked after by Joris Coppens and supervised by the imaging group led by Christian Lohmann.

10 Box 5: Collaborations of NIN within the Netherlands and beyond: Miniscope project.

In late 2016, as part of a NIN-KNAW research fund to foster stronger ties between KNAW institutes, the NIN and NIOO received a grant to capitalize on recent developments that enable cost-effective miniaturized fluorescence microscopes (miniscopes) for functional read-out of brain activity during free-roaming behavior. The NIN was the first academic institution in the Netherlands to provide this open-source technology to its own research groups (Cerebellar mechanisms underlying sleep and motor behavior, Chris De Zeeuw; Compulsive behaviors, Ingo Willuhn). With the help of the Mechatronics Department of the NIN, the miniscope has been disseminated to a wide number of collaborators in the Netherlands (Erasmus MC, VU CNCR, and UMC Utrecht). In 2017, the NIN took a leading role in the further development of the technology, specifically, downscaling the technology, designing and producing in-house electronics and pushing the limits of improved sensitivity and small footprint. To this end, the NIN has invested in 3D rapid prototyping. As part of such efforts, collaborations have been initiated (University of Stuttgart, Erasmus MC and TU Delft) to develop optical and electronic components for two-color and wire-free miniscopes that will be shared with the scientific community.

Figure III: Open-source miniscopes in use and under development at the NIN. Top: Imaging of the cerebellum reveals activity patterns of Purkinje cells during free-roaming behavior. Bottom UCLA design and new NIN prototype, in which the size is reduced further, allowing multiple implants on a single mouse. Moreover, in 2016 the NIN received financial support from the KNAW to further develop the miniscope-approach for imaging in freely moving animals in the Netherlands (Box 5). The electron microscope (EM) facility has been merged with the EM facilities of VU and AMC and is now located at the AMC, where four EM setups are available.

Teaching of PhD students Most PhD students at the institute take part in the Graduate School Neurosciences Amsterdam–Rotterdam (ONWAR), a collaboration between the universities of Amsterdam and Rotterdam and the NIN. A few take part in other graduate schools. The ONWAR‘s training program provides a comprehensive overview of the neurosciences. There are neuroscience courses, the Swammerdam lectures series, annual retreats and general courses (e.g. on statistics and project planning). NIN scientists are actively involved in ONWAR committees and (co-) organize many of the courses. The training program consists of OBTAINING A 405 hours spread over 4 years, and includes ONWAR courses and events, but leaves flexibility for students PHD DEGREE to follow courses at other organizations. ONWAR courses are evaluated and improved where necessary. At most universities, the Questionnaires are used to determine whether new minimal research courses are needed. requirement for obtaining At the onset of the PhD program, the goals of the the PhD degree is one research project and the courses to be followed are published first authorship defined in an education plan. Each PhD student has a article in an international second supervisor with whom progress is monitored journal, and three more annually in a discussion between the candidate, the articles in preparation or supervisor and the co-supervisor. The outcome of the experimental chapters to discussion is documented as an amendment to the which the PhD student education plan. In addition, ONWAR assigns a tutor to each PhD student, who can help or give advice in the made a significant event of problems between supervisor and PhD contribution. students. Currently, many PhD students take more than 5 years to graduate (Appendix 7). Some of these delays are caused by the period of approximately 6 months between the completion of the thesis and the actual defense, and some PhD students postpone their defense when they embark on their first postdoc position. Another cause is the increasing pressure to produce high impact papers, while the minimal requirements set by the universities (4 experimental chapters) are not reduced accordingly. We expect that the institute’s monitoring system will reduce the duration of the PhD program. Furthermore, the PIs have to ask the board for permission whenever the duration of the appointments of PhD students exceeds four years. Shortening of the duration is important because the European trend is to reduce it to 3 years. Discussions are ongoing with the Universities to define a better balance of quality and quantity requirements.

11 Figure 4: Current employment positions of PhD students and Postdocs of the NIN for 2011-2017. The majority stays in science and a very high fraction are employed (unemployed are part of the “other” category). The NIN, the ONWAR and the KNAW organize career events for PhD students to familiarize them with the career opportunities after graduation, and to bring them in contact with people working in companies and academic institutions of interest. Of all PhD students who received their degree between 2011 and 2017, 59% stayed in science, others went into medicine, industry and government (Figure 4). Education of staff The NIN has a special training program for the education of staff. The available budget is k€ 42/year and it can be used for both in-house courses and external courses. Examples of such courses are laboratory animal training courses, language courses and programming courses. The institute also organizes career planning and guidance events for postdocs.

Research Integrity The NIN has created an open research culture with multiple checks and balances regarding the integrity of researchers and the validity of new results. Early experimental results are shared in meetings within the research groups and once the data are ready for publication they are usually presented at the weekly Neuroscience Symposium. As guiding principles for research integrity, the institute adopts the Netherlands Code of Conduct for Academic Practice and the “Advisory Memorandum on Scientific Integrity” published by the KNAW in 2005. Many of the younger researchers are trained to understand issues that can occur with respect to research integrity (e.g. an obligatory meeting with their supervisors about this topic for PhD students that defend their thesis at the VU). To further increase the awareness for issues related to research integrity the institute organizes events on this topic, for example, a presentation by Frans van Lunteren in February 2018. The KNAW also implemented a complaint procedure for its employees when there are questions related to scientific integrity, although the NIN does not yet have experience with this procedure. Open data Publicly funded research data are a public good, produced in the public interest, which should be made openly available with as few restrictions as possible in a timely and responsible manner. The institute has adopted a data policy that ensures safe, accountable, and efficient data storage and that encourages data-sharing. This policy describes the responsibilities of researchers in storing and maintaining datasets and how to do so according to Fair Data Principles. It also describes that each project should have a data management plan, describing data maintenance and storage. The aim of the institute is to have all publications (100%) open access in 2019 (gold or green road). The institute promotes the publication of raw data because it will allow other researchers to check the analysis and conclusions of publications and to re-use data to address different research questions. The institute is currently exploring the new ways in which the data can be published and to that aim a data-steward has been appointed.

A pilot-project has been initiated by the data steward to develop a novel approach for storing and organizing data, independent of its source or nature, which greatly facilitates data sharing. This will be carried out in collaboration with the Human Brain Project and SURFsara.

Diversity Diversity increases creativity, productivity and adaptability, and promotes better mentoring and coaching, collaboration and loyalty. It is therefore a priority of the institute for the coming years to foster and promote diversity in terms of nationalities, ethnicity and gender. At the level of PhD students and postdocs, the institute’s composition is diverse. The institute hosts postdocs and PhDs from 27 nationalities (Appendix 4), with 29% of the scientists from outside the Netherlands, 18% from outside Europe, and 50% females. The institute is rigorously bilingual: all written communication is in both English and Dutch, and most of the meetings are in English. Secretarial staff is at hand to help with translations. A housing officer helps staff coming from abroad to find housing in Amsterdam. Monthly introductory meetings are organized to familiarize newcomers with the institute's rules, and new people are introduced to the NIN community during the weekly institutional symposia. At the PI level, the institute aims to increase diversity, with gender diversity close to the national average (24% where 19% is the percentage of female professors in the Netherlands) 2 , and with group leaders from multiple nationalities but all western European. The institute’s target is to reach at least 30% of female PIs and to attract PIs with a non-European origin in the next 10 years. The following steps have been taken to increase diversity: a non-Dutch female PI was hired, and a new position will be advertised, encouraging international female PIs to apply (increasing the proportion of female PIs to 28%). Finally, workshops about bias awareness and bias management took place in previous years and are planned for 2018 and later to monitor developments on how to promote diversity.

Housing of the NIN An evaluation of the housing situation of all KNAW institutes concludes that, compared to other KNAW institutes, the building of the NIN is inflexible, not very functional or appealing, and in a relatively poor state of maintenance. Furthermore, the institute is divided over two buildings connected by a bridge, which is not beneficial for the overall level of collaboration.

2 https://www.scienceguide.nl/2017/12/monitor-vrouwen-academie/

Necessary construction work is usually delayed by many months - sometimes even by years - because it requires approval of the landlord, the AMC, whose approval process is slow and complicated. The institute has secured the help of the KNAW for improving the housing situation and different scenarios are under investigation, ranging from extensive renovation to a new building. A new or renovated building will be highly beneficial for the overall level of collaboration between the research groups. Uncoupling the building from the AMC’s building license system would increase the institute’s competitiveness when experiments need the creation of new set ups and associated construction work. Two scenarios for the future housing situation are illustrated in Figure 5 (see also Appendix 8).

Figure 5: Housing situation of the NIN. Left, the institute is divided between the R-North and IWO building. The Spinoza Center is adjacent to the NIN. In collaboration with the KNAW, the institute is now considering options for improvement. Two of the scenarios have been illustrated below: the green floors would be occupied by the NIN. A third option is to create a new building

SWOT: Analysis of Strengths, Weaknesses, Opportunities and Threats A clear Strength is the high-level research program and the scientific output and impact, which is excellent. The same holds true for the ability of researchers to attract funding. The research program, with its focus on the role of functional brain circuits, strikes the right balance (neither too narrow nor too broad), enables strong collaborations between the groups and has reached sufficient scientific mass. Furthermore, the institute has been able to build and support facilities that are state-of-the-art, including methods for cellular imaging and high-resolution magnetic resonance imaging, many of which are used by a wide variety of academic and business partners both at home and abroad. The institute has reached a financial situation that is sustainable and has freed up budget to attract a new group to complement the present research program. The main Weakness of the institute is the current housing situation. The institute is composed of several buildings linked by indoors and outdoors bridging structures and corridors. Moreover, there is no clear single entrance with a reception at the ground floor, which hampers not only visibility and outreach, but also the safety of the institute.

The location of the NIN is suboptimal in that it is situated in a remote location that discourages working at night or at the weekend. Finally, installing new connections for electricity, water, air or gas is difficult and cumbersome under the current landlord (AMC). An Opportunity is the plan of the Dutch government to invest more in research in the coming years. An important framework that will determine how the extra funding is spent is given by the National Research Agenda and also by the so-called Top Sector policy. The research of the NIN fits very well within a number of tracks of the National Research Agenda, including the NeuroLabNL route. In addition, the NIN coordinates the consortium “NeuroTech-NL” that aligns with the Top Sectors Life Science and Health and High Tech Systems and Materials and aims to generate new invasive devices for patients, including a visual prosthesis for the blind. A clear Threat is the recent announcement of the AMC to completely renovate the IWO building, in which the majority of our animal research takes place. The renovation, which is planned for the next few years, will take at least two years. Currently, it is not clear if, when and where potential replacement housing is available. Given the importance of continuing our research in a timely fashion for both current and future projects and grants, it is of paramount importance to deal with this clear and present danger. In this regard it should be noted that the breeding of rodents, let alone the training and learning experiments, will be severely impaired if it is has to be done in the vicinity of a construction site.