The Beddington Medal is the BSDB’s major commendation to promising young biologists, awarded for the best PhD thesis in Developmental Biology defended in the year previous to the award. Rosa Beddington was one of the greatest talents and inspirational leaders in the field of developmental biology. Rosa made an enormous contribution to the field in general and to the BSDB in particular, so it seemed entirely appropriate that the Society should establish a lasting memorial to her. The design of the medal, mice on a stylised DNA helix, is from artwork by Rosa herself. We would like to congratulate the 2018 winner of the Beddington Medal, Emilia Favuzzi, and would like to take this opportunity to give a brief overview of her career and her PhD project that was awarded the Beddington medal.

Emilia’s career and project

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The key results of our recent paper in Nature Cell Biology

Cell polarization defines the spatial biological specificities in a cell. During the first cell cycle of a C. elegans zygote, its symmetry is broken by local remodeling of the cortical actomyosin network. This leads to a segregation of the dedicated polarity regulators, the PAR proteins, into two discrete cortical domains. However, it remains unclear how the mechanical changes driven by actomyosin contractions are transmitted to PAR proteins, and this regulates cellular spatial patterning. In our paper, we revealed that both actomyosin contractions and CDC-42 activity modulate the dynamics of the anterior PAR proteins (aPARs) through stimulation of their clustering at the cell cortex. In the early phase of polarity establishment, contractility of the actomyosin cytoskeleton drives cortical tension, which promotes clustering of PAR-3 (Mov.1, Fig.1). In turn, PAR-3 clusters recruit PKC-3, whereas CDC-42 activity antagonizes PKC-3 clustering during later phase of polarization (Mov.2, Fig.2). The degree of aPARs clustering is significantly associated with the stagnation of aPARs exchange at the cortex, and an effective entrainment with the advective flows of the cortical actomyosin network. This is the first report showing that the cell polarity protein PAR-3 is mechanosensitive, and senses forces to form higher order structures at the cell cortex. These findings depict how actomyosin and PAR proteins interplay and set up asymmetry (Fig.3). This feature may also play a role in other cell patterning events including neuron maturation, wound healing and cancer formation.

Movie 1: Cortical PAR-3::GFP (green) and NMY-2::mKate2 (magenta) during the first cell cycle of a C. elegans embryo.

How I started this project

I had made up my mind to become a researcher during my undergraduate days, after first trying to do a simple plasmid construction in a biological laboratory. Back then I was fascinated by all the equipment and materials in the lab. I went on to obtain my Master’s and Ph.D. degrees in Virology and Neuroscience respectively, before moving to Singapore to commence my first postdoctoral training in Frederic Bard’s lab at the Institute of Molecular and Cell Biology (IMCB), A*STAR. There, I matured as a scientist, and with access to multiple advanced microscopes across the various institutes within the campus, I was able to develop my working skills and knowledge in live-imaging techniques. These abilities, have turned out to be a great help in my career so far.

Before joining Fumio Motegi’s lab at the Temasek Lifesciences Laboratory (TLL), I had worked for over 10 years using cell culture to address different biological questions. So, I had a strong feeling that I must do something different for my next post-doc training. However, it was only after Fumio showed a fantastic movie depicting how anterior and posterior PARs are segregated in worm embryos that I decided to pursue this new area of study. My interests had been captured by how complex, yet exquisite, the underlying regulations can be. After I started working on this project and got some beautiful images of the genome-edited GFP-tagged aPARs, which were generous gifts from Kenneth Kemphus from the Cornell University, I realized that C. elegans is such a powerful tool with which we can address fundamental and important questions. I was also encouraged by the worm society, who kindly shared their materials and information, and welcomed me as a newcomer in their community. I was confident that this was what I wanted to do.

How I found the key results in this paper

The first Eureka moment came when I was inspecting the cortical PAR-3::GFP and PKC-3::GFP in wild-type embryos. They showed beautiful and dynamic puncta structures. This led us to further characterize the implication of those puncta during polarity establishment. We then conducted intensive examinations on the clustering of aPARs in wild-type and polarity-mutant zygotes. Another moment of insight came to me when my colleague Ms. Tricia Low noticed that PAR-3::GFP may exhibit mechanosensitivity. PAR-3::GFP failed to form clusters in the non-muscle myosin-II (nmy-2) mutant embryos, suggesting actomyosin and PAR-3 clustering were somehow connected. The clues became clearer when we observed another two phenomena. Firstly, in wild-type embryos, PAR-3 did not reside with NMY-2, suggesting that PAR-3 clustering is not caused by the direct recruitment of PAR-3 molecules to actomyosin. Secondly, although PAR-3 was unable to form clusters in nmy-2 zygotes, PAR-3 clustering was restored when the embryos underwent shape changes, with cortical ruffling occurring during the later stage of embryogenesis. This suggested that actomyosin contractility itself was not essential for PAR-3 clustering. Instead, physical properties of the cortex appeared to play a crucial role in the control of PAR-3. Hence, we hypothesized that cortical tension driven by actomyosin could promote PAR-3 clustering. We tested and validated this assumption in worm zygotes, as well as mammalian fibroblasts NIH3T3 cells exogenously expressing C. elegans PAR-3, which is achieved with the fantastic help from Dr. Yukako Nishimura from the Mechanobiology Institute (MBI), Singapore. We found that in both cases, PAR-3 clustering was rescued under hypotonic treatment when myosin wasn’t functional. This is the first report stating that PAR-3 reorganizes to higher-order structures in response to tension!

Movie 2: GFP tagged PAR-3, PKC-3, and CDC-42 during polarity establishment in one-cell C. elegans embryos.

How we build a team to test our hypothetical model

When we discovered that PAR-3 carries mechanosensitivity and that it could sense and respond to changes in tension in worm zygotes, we wanted to validate and replicate this experiment in cultured cells and monitor PAR-3 clustering using a TIRF microscope. In the meantime, we also needed a proper method to quantify and demonstrate the clustering so that we could report its significance under different conditions. To allow the research to progress without delay, we decided to collaborate with researchers outside of our lab. The MBI and the IMCB instantly came to mind. At MBI, there are dozens of experts in the field of physical biology, as well as a comprehensive collection of advanced microscopes. We therefore felt there was no better choice for collaboration. Moreover, I had established tight connections with people in the IMCB during my post-doctoral training there. In particular, with the Computational Bioimage Analysis (CBA) Unit, which is run by truly reliable and efficient staffs who are doing great jobs in image analysis and quantification. I was fortunate to have the opportunity to establish fruitful collaborations across TLL, MBI, and IMCB. Each institute is highly-respected not only in Singapore, but worldwide, for consistently publishing in high-profile journals, and attracting talented scientists from different countries. Singapore had become one of the most splendid research hubs in the world, which is attributed to the massive investment and strong support from the government into the life science realm.

How we struggled to publish our project

I think the most difficult time for us along the journey was when our manuscript was rejected by the journal in December of 2016. The reviewers appreciated the main point of our story, but they thought the quantification method we had used to measure aPARs clustering was insufficient. Time was a big concern as we considered whether to submit to another journal, which might have been the easier path to publication, or stick with the same journal and strengthen our manuscript. We were in a dilemma. But since we were confident in ourselves, and in our story, we immediately made the decision to amend the quantification method and reanalyze all of our images. Fortunately, the results returned by the modified methods were consistent with our previous conclusions. We quickly revised the manuscript and resubmitted to the same journal and it turned out to be a happy ending. We appreciate Dr. Weimiao Yu and Dr. Laurent Gole from the Computational Bioimage Analysis (CBA) Unit of IMCB for their efforts to come up with the modified code, as well as the detailed descriptions for the quantification method, for the revised manuscript. We are also very grateful to the editor and all our reviewers for their constructive comments and positive encouragements to improve our manuscript. We did enjoy the review process. I hope what we had gone through can be an inspiration to those who might currently be struggling in a difficult time like this. What we need to do is to keep calm and believe in yourself.

Publication of our work along with two other groups

We learned there were several groups working on a similar topic since 2016. Fortunately, we maintained unencumbered communication with these groups, through emails or in person during international conferences, and it is truly exciting to see that we have all successfully published our stories in high-impact journals.

The common conclusion drawn by the three groups is that the degree of PAR-3 oligomerization increases during polarity establishment, and this further promotes the formation of aPAR clusters. The clustering of aPARs supports its segregation along with the actomyosin flow. Moreover, single-molecule pull-down in single embryos, as well as particle tracking, were used by Dickinson et al. to demonstrate that clustered PAR-3 is coupled to the cortical flow and phosphorylation by the mitotic kinase PLK-1 prevents PAR-3 from undergoing oligomerization. Furthermore, through a functional assay, Rodriguez et al. showed that PKC-3 inhibition or activation depends on its interaction with pools of PAR-3 or CDC-42, respectively. We found that PAR-3 carries mechanosensitivity that responds to cortical tension driven by actomyosin contraction. It’s genuinely fantastic that all three papers support each other and yet, by employing distinct approaches, present a unique significance to the questions addressed. I believe this can be a good example to encourage those who may also be facing competition in their research.

Several open questions about cell polarisation

The evolutionarily conserved PAR machinery is predominantly localized at the actomyosin cortex, which lies adjacent to the cell membrane. It is likely that the principle we uncovered is applicable to other types of tissue, and other organisms. For instance, it has been shown that self-assembly of the PAR-3 N’-terminal domain is critical for axon specification of neurons. In this case, the direct binding of the oligomerized domain to the microtubule promotes microtubule bundling and stabilization. It would be interesting to test if this formation of higher-order PAR-3 can be promoted by the activation of non-muscle myosin, which in turn changes local cortical tension. Another example is during Drosophila embryogenesis. Here, during the process of dorsal closure, actomyosin repeatedly assembles and disassembles in the epithelial amnioserosa cells. In this case, PAR-3 forms patches and overlaps with myosin at the apicomedial surface to promote actomyosin contraction. It is intriguing to explore whether myosin assembly induces structural changes in PAR-3, and whether this contributes to developmental morphogenesis. Finally, some follow-up questions remain elusive and need to be further addressed. What are the molecular mechanisms by which PAR-3 clustering or CDC-42 activity apply to compete for the PKC-3/PAR-6? How do aPARs clustering and actomyosin activity regulate and feedback to each other with a temporal-spatial precision during cell-cycle progression? It would be exciting to see emerging studies resolving more of the puzzles surrounding cell patterning in response to extrinsic and intrinsic stimulation in the near future.

References

Wang, S.C., Low, T.Y.F., Nishimura, Y., Gole, L., Yu, W. & Motegi, F. Cortical Forces and CDC-42 Control Clustering of PAR proteins for C. elegans Embyonic Polarization. Nat Cell Biol 19, 988–995 (2017).

Dickinson, D. J., Schwager, F., Pintard, L., Gotta, M. & Goldstein, B. A Single-Cell Biochemistry Approach Reveals PAR Complex Dynamics during Cell Polarization. Developmental Cell 42, 416–434.e11 (2017).

Rodriguez, J. et al. aPKC Cycles between Functionally Distinct PAR Protein Assemblies to Drive Cell Polarity. Developmental Cell 42, 1–35 (2017).

Chen, S. et al. Regulation of Microtubule Stability and Organization by Mammalian Par3 in Specifying Neuronal Polarity. Developmental Cell 24, 26–40 (2013).

David, D. J. V., Tishkina, A. & Harris, T. J. C. The PAR complex regulates pulsed actomyosin contractions during amnioserosa apical constriction in Drosophila. Development 137, 1645–1655 (2010).

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The Turing Centre for Living Systems aims at attracting students willing to work in an interdisciplinary life-science environment and with backgrounds in cell or developmental biology, immunology, neurosciences, theoretical physics, biophysics, computer science, bioinformatics, applied mathematics, engineering.

Candidates are asked to select the projects in order of interest (up to 3) and rank them in the application form.

Link to the PDF file.

Deadline for application: 15^th April

Informal enqueries: info@centuri-livingsystems.org

PHD2018-01 – Using single cell transcriptomics to classify neuron types in two brain regions relevant to social behavior: the olfactory bulb and the hippocampal CA2

PHD2018-02 – Visualizing deep hippocampus neuronal functional activity in vivo using ultra-thin 2-photon endoscopes

PHD2018-03 – Understanding uORF functions through dendritic cells biology and computational approaches

PHD2018-04 – Using higher-order biological networks to explore temporal patterns in cell cycle control

PHD2018-05 – 3D optical microscopy for quantifying T lymphocyte activation

PHD2018-06 – Life and death of Salmonella-containing vacuoles

PHD2018-07 – Dynamics of a self-organized multicellular system

PHD2018-08 – Bacterial adaptation by OXPHOS dynamics: from single cell biology to gut microbiota

PHD2018-09 – Emerging near-infrared chromophores for photoacoustic bio-imaging

PHD2018-10 – Fluid-induced self-organization of ciliated-cell activity in human lungs

PHD2018-11 – Muscle building: bridging molecular order to macroscopic morphogenesis

PHD2018-12 – Deciphering the activation states of plasmacytoid dendritic cells, their dynamical relationships and their molecular regulation

PHD2018-13 – Mathematic modelling of cell migration in confined domains

PHD2018-15 – A versatile virtual reality system to understand animal navigation

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The DRSC/TRiP-Functional Genomics Resources is a Drosophila community resource with three main focus areas: (1) cell-based Drosophila cell screening, (2) fly stock production, and (3) bioinformatics. Our TRiP fly stock production platform is taking nominations for production of CRISPR sgRNA fly stocks. Researchers can nominate genes for knockout (TRiP CRIPSR-KO) or activation (TRiP CRISPR-OE), or both. To search existing and in-production stocks, and to nominate genes for production of new stocks, please visit the gRNA Tracker website. In keeping with our long-time policies, all fly stocks are deposited to the Bloomington Drosophila Stock Center. We look forward to continuing to serve the needs of Drosophila developmental biologists and others through this effort!

(2 votes)

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Applications are invited from outstanding individuals to work under the supervision of Dr Rui Monteiro, Birmingham Fellow, on a BHF funded research project to study the role of TGFb signalling in angiogenic and haemogenic endothelial cell programming. The Monteiro Lab are interested in learning how extrinsic signalling impinges on lineage fate decisions in development and how progenitors and stem cells carry out those decisions, with a particular emphasis on the Transforming Growth Factor β (TGFβ) pathway. Previous work in the lab demonstrated that TGFb1 and TGFb3 play different roles in programming haemogenic endothelium to become of blood stem cells in vivo (Monteiro et al, 2016). The Research Fellow will study the gene regulatory network that carries out the ligand-specific functions for TGFb1 and TGFb3 ligands in haemogenic and angiogenic endothelium in vivo. They will make use of several approaches, including genome editing with CRISPR/Cas9, transgenesis, fluorescence activated cell sorting and transcriptional and epigenetic profiling using zebrafish as a model.

The successful applicant will have a first degree and a PhD in developmental biology, molecular genetics, biology or in a related discipline relevant to the project. They will also have a strong background in molecular biology and previous experience with model organism and/or analysis of transcriptomic and epigenetic data.

Informal enquiries should be directed to Dr. Rui Monteiro (R.Monteiro@bham.ac.uk)

Starting salary is normally on Grade 7 according to experience.

Closing date: 10 March 2018            Reference:  58652

To download the details of this position and submit an electronic application online please go to https://www.birmingham.ac.uk/staff/jobs/index.aspx. Please quote the appropriate Job Ref in all enquiries, alternatively information can be obtained from www.hr.bham.ac.uk

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PD2018-03 – Computational study of cell pattern emergence in embryonic and tumorigenic tissues

Project abstract – The ability of cells to self-organize into patterned tissues composed of multiple cell types is central to animal morphogenesis and relies on both biological and physical factors. We propose to investigate numerically and from a biophysical point of view the pattern formation observed in two different complex tissues respectively characterised by their stereotyped vs seemingly disorganised structure: the embryonic epithelium of Xenopus (with A. Pasini) and Drosophila brain tumors (with C. Maurange).

In Xenopus, we will study how multiciliated cells (MCCs) distribute in a regularly spaced pattern during intercalation into an epithelial layer, and explore how the pattern is established and maintained through a balance between mutual repulsion among MCCs and attraction between MCCs and epithelial layer cells. In Drosophila, we will study how clusters of brain cancer stem cells (CSCs) form and how they affect tumor progression. We will investigate how physical (tension, adhesion) and biochemical (growth and differentiation factors) cues contribute to segregate clusters of cells with different self-renewing potentials, regulate their size distribution and density, and thus determine tumor growth rate.

The computational tools envisaged for the project involve the numerical implementation of energy minimization algorithms such as the Cellular Potts Model (with R. Clément). We plan to model both systems with an energy function encompassing the different biological and physical interactions suspected to play a role in the processes. Such energy functions can comprise adhesion, tension, affinities or repulsions among cell types. Motility and cell proliferation can also be implemented at given rates, depending on cell types. Models with be implemented in light of the experimental results, and we expect that simulations will in turn guide the design of new biological experiments.

Expected profile – Candidates should have a robust background in physics and numerical simulations, and ideally be familiar with the Potts Model and its cellular version. As the project is strongly interdisciplinary and involves close collaboration with experimental biologists, previous experience in developmental biology or biophysics will be appreciated. A strong interest in biological questions, in particular in the principles of morphogenesis, is mandatory.

Scientific environment – The recruited post-doc will benefit from a world-class interdisciplinary environment, both within the IBDM (Marseilles Institute for Developmental Biology) and among the other institutes taking part into the CENTURI program.

Supervisors

Raphaël Clément (raphael.clement@univ-amu.fr)- IBDM, UMR 7288 – Cell and tissue physics – Team Lenne

Cédric Maurange (cedric.maurange@univ-amu.fr)- IBDM, UMR7288 – Neural stem cell plasticity – Team Maurange

Andrea Pasini (andrea.pasini@univ-amu.fr) – IBDM, UMR7288 – Biology of ciliated epithelia – Team Kodjabachian

Deadline for application: 28th February

Please apply online on the Centuri website.

Recruitment Form – PD2018-03 – Computational study of cell pattern emergence in embryonic and tumorigenic tissues

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A postdoctoral position is available to study mechanisms of Sonic Hedgehog signal transduction in Stacey Ogden’s lab at St. Jude Children’s Research Hospital, Memphis, TN. The successful candidate will join a collaborative work group aimed at understanding how the Sonic Hedgehog pathway is regulated during development, and dissecting how its regulation is usurped in cancer. Areas of interest include biogenesis and secretion of the Hedgehog family ligands, contributions of lipid metabolism to pathway activity, regulation and signaling of the signal transducer Smoothened and investigation of the downstream effectors to which it signals. Research projects in the lab will entail use of biochemical and cell biological techniques and mouse model systems.

Applicants should have or expect a PhD degree at the time of application. The selected postdoctoral fellow will actively develop their own research project, perform laboratory experiments with minimal supervision, develop new procedures as needed and interact collaboratively with other members of the lab. The successful candidate will also actively participate in the publication and presentation of research results. Prior experience with signal transduction research, lipid metabolism or mouse model systems is preferred.

www.stjude.org/ogden

Email: Stacey.ogden@stjude.org

Phone: 901-595-6281

Application website: https://postdoc-stjude.icims.com/jobs

Job number: 38158

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The San Francisco Declaration on Research Assessment (DORA) was conceived in 2012 at an ASCB meeting, and has since its launch in 2013 has garnered thousands of signatories from individuals and organisations. Its aim is to improve the way in which the quality of research output is evaluated, with a key recommendation being the elimination of journal-based metrics by funding agencies, institutions and publishers when judging research and researchers.

This year, DORA has had something of an upgrade: with the support of organisations including the Company of Biologists (the not-for-profit publisher that runs Development and funds the Node!), DORA now has a full time Community Manager Anna Hatch, a new steering committee, and a new website.

To find out more about these developments, we caught up with Stephen Curry, who chairs the DORA steering committee and is Professor of Structural Biology and Assistant Provost for Equality, Diversity and Inclusion at Imperial College London.

Hi Stephen! Can you tell us a bit about your science?

I’m a structural biologist and primarily use protein crystallography to work out the three-dimensional structures of interesting macromolecules. My main research efforts have been focused on virus and host-cell proteins involved in the replication of RNA viruses – principally foot-and-mouth disease virus and noroviruses. But I am in the process of winding down my research lab so that I can concentrate on other interests (discussed below) and my new role as Assistant Provost for Equality, Diversity and Inclusion at Imperial College.

You’re also passionate about science advocacy and communication – you are Vice Chair of the Science is Vital campaign group, contribute to The Guardian’s science blog Occam’s Corner, and have 16k followers on Twitter. Has this side of science – away from the lab bench – always been important to you?

It’s always been important but I’ve only really been properly active in this space since 2008 when I started my blog. I found that writing about science really made me think about what it means to be a scientist in 21^st century Britain and that led me to learn a lot about scientific publishing and research funding, both of which are tied in rather convoluted ways to the business of research assessment. I have enjoyed getting involved in these debates and in campaigns to bring about positive change. Being involved in Science it Vital right from the very beginning has been a fantastic lesson in what can be done with modern communication tools if you just knuckle down and get organised.

You were one of the original signatories to DORA – why was DORA necessary in 2013?

It was already overdue in 2013. I wasn’t involved in the formulation of the declaration but was invited to sign prior to the launch and didn’t hesitate to do so. I had already become aware of the perverting effects of journal impact factors on science and scientists’ careers. And I knew that many other people shared my concerns. My 2012 blogpost, Sick of Impact Factors, remains on of the most ‘popular’ that I have ever written. It clearly struck a nerve.

And what do you think has been achieved in the years since then?

DORA has been really helpful in re-focusing the conversation on how the scientific community does research assessment. Without anyone designing the system, journal metrics have been co-opted for the evaluation of individuals to such a degree that publication in certain tiles (infamously Nature, Cell and Science in the biomedical sciences) are now seen as the key to success. DORA has helped to challenge that view – though we should certainly be mindful of parallel work on the Leiden Manifesto and The Metric Tide report (on which I was a co-author). So I think there is much greater awareness of the nature of the problem now and even some tentative steps to address it.

So what’s new – what does DORA’s new lease of life entail?

What’s new is that DORA now has a much higher level of material and financial support (from 9 organisations: ASCB, Company of Biologists, CRUK, eLife, EMBO, F1000, Hindawi, PLoS, and Wellcome). That has allowed us to hire a full-time community manager (Dr Anna Hatch) and refresh the steering group, which I now chair. We’ve also refreshed out web-site and have a new, easy-to-find URL (sfdora.org). This will allow us to raise the profile of DORA – we mean to get the word out much more proactively – but we are also determined to make a renewed effort to ignite the discussion around what constitutes robust and effective research assessment. We know that to change practice we need to figure out practical ways to help busy reviewers sift through job and grant applications and CVs without falling back on mis-use of the JIF.

Personally, what has it been like to be involved with DORA – is it challenging to get consensus from such a broad group of scientists and organisations?

There’s a lot of work to do because there is always resistance to change. DORA is not out to name and shame people or organisations that haven’t signed. But we want to challenge them to think about research assessment and do what we can to help them find a way forward. We aim to do a much more comprehensive job of discovering and disseminating good practice from around the world.

Why (and how) should young researchers get involved in DORA?

Because bad research assessment leads to bad research. DORA’s focus on improving research assessment fits very well with the ambitions that first attracts early career researchers to research: to understand and change the world. We will do that best if we are doing a proper job of recognising and rewarding the best research. That’s not just about publishing the best science (irrespective of journal name), but also meshes with parallel concerns about open science, data and code sharing and efforts to address deepening concerns about reproducibility, which are at least partly due to our over-reliance on metrics such as the JIF for judging individuals. However, we cannot simply expect young researchers to take the responsibility for change; it is up to the old guard (people like myself) and organisations like DORA to provide real support.

Further DORA articles:

Stephen Curry’s World View in Nature

https://www.nature.com/articles/d41586-018-01642-w

Research Councils UK Press release:

http://www.rcuk.ac.uk/media/news/180207/

Research Councils UK statement on responsible metrics:

http://www.rcuk.ac.uk/documents/research/rcuk-statement-on-the-responsible-use-of-metrics-in-research-assessment-pdf/

Times Higher Education also wrote a story about DORA

https://www.timeshighereducation.com/news/funding-councils-sign-responsible-research-assessment#survey-answer

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