Metric Ion Classification (MIC): A deep learning tool for assigning ions and waters in cryo-EM and x-ray crystallography structures

Kavli Affiliate: Michael Keiser | Authors: Laura Shub, Wenjin Liu, Georgios Skiniotis, Michael J. Keiser and Michael J. Robertson | Summary: At sufficiently high resolution, x-ray crystallography and cryogenic electron microscopy are capable of resolving small spherical map features corresponding to either water or ions. Correct classification of these sites provides crucial insight for understanding […]


Continue.. Metric Ion Classification (MIC): A deep learning tool for assigning ions and waters in cryo-EM and x-ray crystallography structures

Single neurons and networks in the claustrum integrate input from widespread cortical sources – Copy

Kavli Affiliate: Kristofer Bouchard | Authors: Jiali Lu, Sumithra Surendralal, Kristofer E Bouchard and Dezhe Z. Jin | Summary: Generative models have broad applications, ranging from language processing to analyzing bird-song. In this study, we demonstrate how a statistical test, designed to prevent overgeneralization in sequence generation, can be used to deduce minimal models for […]


Continue.. Single neurons and networks in the claustrum integrate input from widespread cortical sources – Copy

Dynamic fibroblast-immune interactions shape wound healing after brain injury

Kavli Affiliate: Anna Molofsky and Jeanne Paz | Authors: Nathan A. Ewing-Crystal, Nicholas M. Mroz, Anthony A. Chang, Eric Dean Merrill, Sofia E. Caryotakis, Leon Teo, Amara Larpthaveesarp, Tatsuya Tsukui, Aditya Katewa, Remy Pennington, Gabriel L. McKinsey, Sophia Nelson, Agnieszka Ciesielska, Madelene W. Dahlgren, Helena Paidassi, Saket Jain, Manish K. Aghi, James A. Bourne, Jeanne […]


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Small molecule and cell contact-inducible systems for controlling expression and differentiation in stem cells

Kavli Affiliate: Hana El-Samad | Authors: Sarah S. Soliman, Devan H. Shah, Hana El-Samad and Zara Y. Weinberg | Summary: Synthetic developmental biology uses engineering approaches to understand multicellularity with goals ranging from recapitulating development to building synthetic organisms. Current approaches include engineering multicellular patterning, controlling differentiation, and implementing cooperative cellular behaviors in model systems. […]


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SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition

Kavli Affiliate: Robert Edwards | Authors: Qianyi E Zhang, Jared Lindenberger, Ruth Parsons, Bhishem Thakur, Rob Parks, Chan Soo Park, Xiao Huang, Salam Sammour, Katarzyna Janowska, Taylor N Spence, Robert J. Edwards, Mitchell Martin, Wilton B Williams, Sophie Gobeil, David C Montefiori, Bette Korber, Kevin O’Neil Saunders, Barton F Haynes, Barton F. Haynes, Rory Henderson […]


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Cell type-specific dynamics of prefrontal gamma synchrony during flexible behavior

Kavli Affiliate: Vikaas Sohal | Authors: Aarron Justin Phensy, Lara Louise Hagopian and Vikaas Singh Sohal | Summary: The prefrontal cortex (PFC) is required for many cognitive processes that are disrupted in conditions such as schizophrenia. The PFC is composed of neuronal networks which are organized by both local microcircuitry and inter-regional projections, within which […]


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How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies

Kavli Affiliate: Robert Edwards | Authors: George Bouras, Louise M Judd, Robert A Edwards, Sarah Vreugde, Timothy P. Stinear and Ryan R Wick | Summary: It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing is still required for perfection. However, the effect of short-read depth […]


Continue.. How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies

Human Anterior Insular Cortex Encodes Multiple Electrophysiological Representations of Anxiety-Related Behaviors

Kavli Affiliate: Edward Chang | Authors: Andrew Moses Lee, Virginia Sturm, Heather Dawes, Andrew D Krystal and Edward Chang | Summary: Anxiety is a common symptom across psychiatric disorders, but the neurophysiological underpinnings of these symptoms remain unclear. This knowledge gap has prevented the development of circuit-based treatments that can target the neural substrates underlying […]


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Deep phenotypic profiling of neuroactive drugs in larval zebrafish

Kavli Affiliate: Michael Keiser | Authors: Leo Gendelev, Jack Taylor, Douglas Myers-Turnbull, Steven Chen, Matthew N. McCarroll, Michelle R. Arkin, David Kokel and Michael J. Keiser | Summary: Behavioral larval zebrafish screens leverage a high-throughput small molecule discovery format to find neuroactive molecules relevant to mammalian physiology. We screened a library of 650 central nervous […]


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Inhibition of Indirect Pathway Activity Causes Abnormal Decision-Making In a Mouse Model of Impulse Control Disorder in Parkinson’s Disease

Kavli Affiliate: Alexandra Nelson | Authors: Xiaowen Zhuang, Julia Lemak, Sadhana Sridhar and Alexandra B Nelson | Summary: Healthy action selection relies on the coordinated activity of striatal direct and indirect pathway neurons. In Parkinson’s disease (PD), in which loss of midbrain dopamine neurons is associated with progressive motor and cognitive deficits, this coordination is […]


Continue.. Inhibition of Indirect Pathway Activity Causes Abnormal Decision-Making In a Mouse Model of Impulse Control Disorder in Parkinson’s Disease