@article {140660, title = {A machine-learning tool to identify bistable states from calcium imaging data.}, journal = {J Physiol}, year = {2024}, month = {2024 Mar 14}, abstract = {

Mapping neuronal activation using calcium imaging in vivo during behavioural tasks has advanced our understanding of nervous system function. In almost all of these studies, calcium imaging is used to infer spike probabilities because action potentials activate voltage-gated calcium channels and increase intracellular calcium levels. However, neurons not only fire action potentials, but also convey information via intrinsic dynamics such as by generating bistable membrane potential states. Although a number of tools for spike inference have been developed and are currently being used, no tool exists for converting calcium imaging signals to maps of cellular state in bistable neurons. Purkinje neurons in the larval zebrafish cerebellum exhibit membrane potential bistability, firing either tonically or in bursts. Several studies have implicated the role of a population code in cerebellar function, with bistability adding an extra layer of complexity to this code. In the present study, we develop a tool, CaMLSort, which uses convolutional recurrent neural networks to classify calcium imaging traces as arising from either tonic or bursting cells. We validate this classifier using a number of different methods and find that it performs well on simulated event rasters as well as real biological data that it had not previously seen. Moreover, we find that CaMLsort generalizes to other bistable neurons, such as dopaminergic neurons in the ventral tegmental area of mice. Thus, this tool offers a new way of analysing calcium imaging data from bistable neurons to understand how they participate in network computation and natural behaviours. KEY POINTS: Calcium imaging, compriising the gold standard of inferring neuronal activity, does not report cellular state in neurons that are bistable, such as Purkinje neurons in the cerebellum of larval zebrafish. We model the relationship between Purkinje neuron electrical activity and its corresponding calcium signal to compile a dataset of state-labelled simulated calcium signals. We apply machine-learning methods to this dataset to develop a tool that can classify the state of a Purkinje neuron using only its calcium signal, which works well on real data even though it was trained only on simulated data. CaMLsort (Calcium imaging and Machine Learning based tool to sort intracellular state) also generalizes well to bistable neurons in a different brain region (ventral tegmental area) in a different model organism (mouse). This tool can facilitate our understanding of how these neurons carry out their functions in a circuit.

}, issn = {1469-7793}, doi = {10.1113/JP284373}, author = {Varma, Aalok and Udupa, Sathvik and Sengupta, Mohini and Ghosh, Prasanta Kumar and Thirumalai, Vatsala} } @article {139055, title = {Predictive neural computations in the cerebellum contribute to motor planning and faster behavioral responses in larval zebrafish.}, journal = {Sci Adv}, volume = {10}, year = {2024}, month = {2024 Jan 05}, pages = {eadi6470}, abstract = {

The ability to predict the future based on past experience lies at the core of the brain{\textquoteright}s ability to adapt behavior. However, the neural mechanisms that participate in generating and updating predictions are not clearly understood. Further, the evolutionary antecedents and the prevalence of predictive processing among vertebrates are even less explored. Here, we show evidence of predictive processing via the involvement of cerebellar circuits in larval zebrafish. We presented stereotyped optic flow stimuli to larval zebrafish to evoke swims and discovered that lesioning the cerebellum abolished prediction-dependent modulation of swim latency. When expectations of optic flow direction did not match with reality, error signals arrive at Purkinje cells via the olivary climbing fibers, whereas granule cells and Purkinje cells encode signals of expectation. Strong neural representations of expectation correlate with faster swim responses and vice versa. In sum, our results show evidence for predictive processing in nonmammalian vertebrates with the involvement of cerebellum, an evolutionarily conserved brain structure.

}, keywords = {Animals, Cerebellum, Larva, Neurons, Purkinje Cells, Zebrafish}, issn = {2375-2548}, doi = {10.1126/sciadv.adi6470}, author = {Narayanan, Sriram and Varma, Aalok and Thirumalai, Vatsala} } @article {128573, title = {eLife{\textquoteright}s new model and its impact on science communication.}, journal = {Elife}, volume = {11}, year = {2022}, month = {2022 Dec 08}, abstract = {

The eLife Early-Career Advisory Group discusses eLife{\textquoteright}s new peer review and publishing model, and how the whole process of scientific communication could be improved for the benefit of early-career researchers and the entire scientific community.

}, keywords = {Communication, Peer Review}, issn = {2050-084X}, doi = {10.7554/eLife.84816}, author = {Urban, Lara and De Niz, Mariana and Fern{\'a}ndez-Chiappe, Florencia and Ebrahimi, Hedyeh and Han, Laura K M and Mehta, Devang and Mencia, Regina and Mittal, Divyansh and Ochola, Elizabeth and Paz Quezada, Carolina and Romani, Facundo and Sinapayen, Lana and Tay, Andy and Varma, Aalok and Yahia Mohamed Elkheir, Lamis} } @article {106555, title = {Feeling like a {\textquoteright}real{\textquoteright} scientist.}, journal = {Elife}, volume = {11}, year = {2022}, month = {2022 02 17}, abstract = {

Peer reviewing helped a graduate student to finally gain a sense of belonging within the research community.

}, issn = {2050-084X}, doi = {10.7554/eLife.77719}, author = {Varma, Aalok} } @article {113537, title = {Recommendations for empowering early career researchers to improve research culture and practice.}, journal = {PLoS Biol}, volume = {20}, year = {2022}, month = {2022 Jul 07}, pages = {e3001680}, abstract = {

Early career researchers (ECRs) are important stakeholders leading efforts to catalyze systemic change in research culture and practice. Here, we summarize the outputs from a virtual unconventional conference (unconference), which brought together 54 invited experts from 20 countries with extensive experience in ECR initiatives designed to improve the culture and practice of science. Together, we drafted 2 sets of recommendations for (1) ECRs directly involved in initiatives or activities to change research culture and practice; and (2) stakeholders who wish to support ECRs in these efforts. Importantly, these points apply to ECRs working to promote change on a systemic level, not only those improving aspects of their own work. In both sets of recommendations, we underline the importance of incentivizing and providing time and resources for systems-level science improvement activities, including ECRs in organizational decision-making processes, and working to dismantle structural barriers to participation for marginalized groups. We further highlight obstacles that ECRs face when working to promote reform, as well as proposed solutions and examples of current best practices. The abstract and recommendations for stakeholders are available in Dutch, German, Greek (abstract only), Italian, Japanese, Polish, Portuguese, Spanish, and Serbian.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3001680}, author = {Kent, Brianne A and Holman, Constance and Amoako, Emmanuella and Antonietti, Alberto and Azam, James M and Ballhausen, Hanne and Bediako, Yaw and Belasen, Anat M and Carneiro, Clarissa F D and Chen, Yen-Chung and Compeer, Ewoud B and Connor, Chelsea A C and Cr{\"u}well, Sophia and Debat, Humberto and Dorris, Emma and Ebrahimi, Hedyeh and Erlich, Jeffrey C and Fern{\'a}ndez-Chiappe, Florencia and Fischer, Felix and Gazda, Ma{\l}gorzata Anna and Glatz, Toivo and Grabitz, Peter and Heise, Verena and Kent, David G and Lo, Hung and McDowell, Gary and Mehta, Devang and Neumann, Wolf-Julian and Neves, Kleber and Patterson, Mark and Penfold, Naomi C and Piper, Sophie K and Puebla, Iratxe and Quashie, Peter K and Quezada, Carolina Paz and Riley, Julia L and Rohmann, Jessica L and Saladi, Shyam and Schwessinger, Benjamin and Siegerink, Bob and Stehlik, Paulina and Tzilivaki, Alexandra and Umbers, Kate D L and Varma, Aalok and Walavalkar, Kaivalya and de Winde, Charlotte M and Zaza, Cecilia and Weissgerber, Tracey L} } @article {91958, title = {Creating clear and informative image-based figures for scientific publications.}, journal = {PLoS Biol}, volume = {19}, year = {2021}, month = {2021 Mar 31}, pages = {e3001161}, abstract = {

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in 3 fields; plant sciences, cell biology, and physiology (n = 580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16\%, cell biology 12\%, plant sciences 2\%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3001161}, author = {Jambor, Helena and Antonietti, Alberto and Alicea, Bradly and Audisio, Tracy L and Auer, Susann and Bhardwaj, Vivek and Burgess, Steven J and Ferling, Iuliia and Gazda, Ma{\l}gorzata Anna and Hoeppner, Luke H and Ilangovan, Vinodh and Lo, Hung and Olson, Mischa and Mohamed, Salem Yousef and Sarabipour, Sarvenaz and Varma, Aalok and Walavalkar, Kaivalya and Wissink, Erin M and Weissgerber, Tracey L} }