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December 2021

The mechanism underlying the emergence of a stable alpha band(8-12Hz) oscillation during general anesthesia is still unclear but could result from the network interactions between various brain regions. These regions can generate membrane transition patterns between Up and Dow states. Zonca and Holcman examined the influence of synaptic short-term plasticity on the development of stable oscillations between excitatory and inhibitory neurons using neuronal network models. They report that the alpha-band, emerges spontaneously after excitatory stimuli are shut off. However, fragmentation of the alpha band may result from transitions from Up to Down state or from reducing the synaptic random activity.

Twitter: @LouZonca, @David_Holcman, @HolcmanLab

Image Credit: Lou Zonca and David Holcman, PSL Research University

Editorials

Ten simple rules for effective presentation slides

Kristen M. Naegle

Ten simple rules for scientists getting started in science education

Stephen Pompea, Pedro Russo

Ten simple rules for developing bioinformatics capacity at an academic institution

Shaun Aron, C. Victor Jongeneel, Paballo Abel Chauke, Melek Chaouch, Judit Kumuthini, Lyndon Zass, Fouzia Radouani, Samar Kamal Kassim, Faisal M. Fadlelmola, Nicola Mulder

Perspectives

Ten simple rules for creating a scientific web application

Jessica L. Burnett, Renee Dale, Chung-Yi Hou, Gabriela Palomo-Munoz, Kaitlin Stack Whitney, Steve Aulenbach, Robert Sky Bristol, Denis Valle, Tristan P. Wellman

A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design

Jordan J. Baker, Christopher J. P. Mathy, Julia Schaletzky

Research Articles

RNA editing regulates lncRNA splicing in human early embryo development

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When and why direct transmission models can be used for environmentally persistent pathogens

Lee Benson, Ross S. Davidson, Darren M. Green, Andrew Hoyle, Mike R. Hutchings, Glenn Marion

Dynamic maximum entropy provides accurate approximation of structured population dynamics

Katarína Bod’ová, Enikő Szép, Nicholas H. Barton

Observable variations in human sex ratio at birth

Yanan Long, Qi Chen, Henrik Larsson, Andrey Rzhetsky

Optimal transport analysis reveals trajectories in steady-state systems

Stephen Zhang, Anton Afanassiev, Laura Greenstreet, Tetsuya Matsumoto, Geoffrey Schiebinger

Systematic analysis of noise reduction properties of coupled and isolated feed-forward loops

Suchana Chakravarty, Attila Csikász-Nagy

Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble

Icíar Civantos-Gómez, Javier García-Algarra, David García-Callejas, Javier Galeano, Oscar Godoy, Ignasi Bartomeus

Simulations of dynamically cross-linked actin networks: Morphology, rheology, and hydrodynamic interactions

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Autonomous epithelial folding induced by an intracellular mechano–polarity feedback loop

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The impact of whole genome duplications on the human gene regulatory networks

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Extracting multi-way chromatin contacts from Hi-C data

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Paradoxical relationship between speed and accuracy in olfactory figure-background segregation

Lior Lebovich, Michael Yunerman, Viviana Scaiewicz, Yonatan Loewenstein, Dan Rokni

Hebbian plasticity in parallel synaptic pathways: A circuit mechanism for systems memory consolidation

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Benchmarking of tools for axon length measurement in individually-labeled projection neurons

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GCAEMDA: Predicting miRNA-disease associations via graph convolutional autoencoder

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Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis

Jan Ewald, Flora Rivieccio, Lukáš Radosa, Stefan Schuster, Axel A. Brakhage, Christoph Kaleta

From decision to action: Detailed modelling of frog tadpoles reveals neuronal mechanisms of decision-making and reproduces unpredictable swimming movements in response to sensory signals

Andrea Ferrario, Andrey Palyanov, Stella Koutsikou, Wenchang Li, Steve Soffe, Alan Roberts, Roman Borisyuk

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data

Asa Thibodeau, Shubham Khetan, Alper Eroglu, Ryan Tewhey, Michael L. Stitzel, Duygu Ucar

Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies

Sarah A. Robinson, Matthew I. J. Raybould, Constantin Schneider, Wing Ki Wong, Claire Marks, Charlotte M. Deane

Roles of mTOR in thoracic aortopathy understood by complex intracellular signaling interactions

Ana C. Estrada, Linda Irons, Bruno V. Rego, Guangxin Li, George Tellides, Jay D. Humphrey

Optimal vaccine allocation for COVID-19 in the Netherlands: A data-driven prioritization

Fuminari Miura, Ka Yin Leung, Don Klinkenberg, Kylie E. C. Ainslie, Jacco Wallinga

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

Thomas W. Christy, Catherine A. Giannetti, Alain Laederach, Kevin M. Weeks

How the value of the environment controls persistence in visual search

Michael R. Traner, Ethan S. Bromberg-Martin, Ilya E. Monosov

Statistical tests for intra-tumour clonal co-occurrence and exclusivity

Jack Kuipers, Ariane L. Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko Beerenwinkel

Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant

Joseph R. Larsen, Margaret R. Martin, John D. Martin, James B. Hicks, Peter Kuhn

Subjective optimality in finite sequential decision-making

Yeonju Sin, HeeYoung Seon, Yun Kyoung Shin, Oh-Sang Kwon, Dongil Chung

Acoustic traits of bat-pollinated flowers compared to flowers of other pollination syndromes and their echo-based classification using convolutional neural networks

Ralph Simon, Karol Bakunowski, Angel Eduardo Reyes-Vasques, Marco Tschapka, Mirjam Knörnschild, Jan Steckel, Dan Stowell

One-carbon metabolism during the menstrual cycle and pregnancy

Ruby Kim, H. Frederik Nijhout, Michael C. Reed

Preparing to move: Setting initial conditions to simplify interactions with complex objects

Rashida Nayeem, Salah Bazzi, Mohsen Sadeghi, Neville Hogan, Dagmar Sternad

A spatio-temporal model to reveal oscillator phenotypes in molecular clocks: Parameter estimation elucidates circadian gene transcription dynamics in single-cells

Måns Unosson, Marco Brancaccio, Michael Hastings, Adam M. Johansen, Bärbel Finkenstädt

Revealing mechanisms of infectious disease spread through empirical contact networks

Pratha Sah, Michael Otterstatter, Stephan T. Leu, Sivan Leviyang, Shweta Bansal

Internal state effects on behavioral shifts in freely behaving praying mantises (Tenodera sinensis)

Shanel C. Pickard, David J. Bertsch, Zoe Le Garrec, Roy E. Ritzmann, Roger D. Quinn, Nicholas S. Szczecinski

Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples

Priit Paluoja, Hindrek Teder, Amin Ardeshirdavani, Baran Bayindir, Joris Vermeesch, Andres Salumets, Kaarel Krjutškov, Priit Palta

Multiscale model for forecasting Sabin 2 vaccine virus household and community transmission

Michael Famulare, Wesley Wong, Rashidul Haque, James A. Platts-Mills, Parimalendu Saha, Asma B. Aziz, Tahmina Ahmed, Md Ohedul Islam, Md Jashim Uddin, Ananda S. Bandyopadhyay, Mohammed Yunus, Khalequ Zaman, Mami Taniuchi

Stress generation, relaxation and size control in confined tumor growth

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Corrections

Correction: Practical considerations for measuring the effective reproductive number, Rt

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