Mathematics and computing

  • Article
    | Open Access

    Relapse, reinfection and recrudescence can all cause recurrent infection after treatment of Plasmodium vivax malaria in endemic areas, but are difficult to distinguish. Here the authors show that they can be differentiated probabilistically and thereby demonstrate the high efficacy of primaquine treatment in preventing relapse.

    • Aimee R. Taylor
    • , James A. Watson
    • , Cindy S. Chu
    • , Kanokpich Puaprasert
    • , Jureeporn Duanguppama
    • , Nicholas P. J. Day
    • , Francois Nosten
    • , Daniel E. Neafsey
    • , Caroline O. Buckee
    • , Mallika Imwong
    •  & Nicholas J. White
  • Article
    | Open Access

    Compared to single nucleotide variants and short indels, structural variants (SVs) are often more challenging to detect using high-throughput sequencing based methods. Here, the authors develop LinkedSV, a computational tool for SV detection using linked-read exome and genome sequencing data.

    • Li Fang
    • , Charlly Kao
    • , Michael V. Gonzalez
    • , Fernanda A. Mafra
    • , Renata Pellegrino da Silva
    • , Mingyao Li
    • , Sören-Sebastian Wenzel
    • , Katharina Wimmer
    • , Hakon Hakonarson
    •  & Kai Wang
  • Perspective
    | Open Access

    Recent research in motor neuroscience has focused on optimal feedback control of single, simple tasks while robotics and AI are making progress towards flexible movement control in complex environments employing hierarchical control strategies. Here, the authors argue for a return to hierarchical models of motor control in neuroscience.

    • Josh Merel
    • , Matthew Botvinick
    •  & Greg Wayne
  • Article
    | Open Access

    t-SNE is widely used for dimensionality reduction and visualization of high-dimensional single-cell data. Here, the authors introduce a protocol to help avoid common shortcomings of t-SNE, for example, enabling preservation of the global structure of the data.

    • Dmitry Kobak
    •  & Philipp Berens
  • Article
    | Open Access

    Haplotype information inferred by phasing is useful in genetic and genomic analysis. Here, the authors develop SHAPEIT4, a phasing method that exhibits sub-linear running time, provides accurate haplotypes and enables integration of external phasing information.

    • Olivier Delaneau
    • , Jean-François Zagury
    • , Matthew R. Robinson
    • , Jonathan L. Marchini
    •  & Emmanouil T. Dermitzakis
  • Article
    | Open Access

    Structural variants may be omitted in sequence analysis despite their importance in genome variation and phenotypic impact. Here the authors present GraphTyper2, which uses pangenome graphs to genotype structural variants using short-reads and can be applied in large-scale sequencing studies.

    • Hannes P. Eggertsson
    • , Snaedis Kristmundsdottir
    • , Doruk Beyter
    • , Hakon Jonsson
    • , Astros Skuladottir
    • , Marteinn T. Hardarson
    • , Daniel F. Gudbjartsson
    • , Kari Stefansson
    • , Bjarni V. Halldorsson
    •  & Pall Melsted
  • Article
    | Open Access

    Reconstructing system dynamics on complex high-dimensional energy landscapes from static experimental snapshots remains challenging. Here, the authors introduce a framework to infer the essential dynamics of physical and biological systems without need for time-dependent measurements.

    • Philip Pearce
    • , Francis G. Woodhouse
    • , Aden Forrow
    • , Ashley Kelly
    • , Halim Kusumaatmaja
    •  & Jörn Dunkel
  • Article
    | Open Access

    Network properties can be modified when they interact with other networks, yet most previous results have focused on equilibrium states exclusively. Here the authors introduce a framework to examine the out-of-equilibrium dynamics of evolutionary processes to mimic real-world interconnected networks.

    • Javier M. Buldú
    • , Federico Pablo-Martí
    •  & Jacobo Aguirre
  • Article
    | Open Access

    People are able to mentally time travel to distant memories and reflect on the consequences of those past events. Here, the authors show how a mechanism that connects learning from delayed rewards with memory retrieval can enable AI agents to discover links between past events to help decide better courses of action in the future.

    • Chia-Chun Hung
    • , Timothy Lillicrap
    • , Josh Abramson
    • , Yan Wu
    • , Mehdi Mirza
    • , Federico Carnevale
    • , Arun Ahuja
    •  & Greg Wayne
  • Article
    | Open Access

    Imaging heart development is challenging due to constant tissue movement and changing physical landmarks. Here the authors present an algorithm capable of maintaining phase-locked imaging throughout a 24 hour timespan, enabling long term timelapse imaging studies of zebrafish heart development, repair and regeneration.

    • Jonathan M. Taylor
    • , Carl J. Nelson
    • , Finnius A. Bruton
    • , Aryan K. Baghbadrani
    • , Charlotte Buckley
    • , Carl S. Tucker
    • , Adriano G. Rossi
    • , John J. Mullins
    •  & Martin A. Denvir
  • Article
    | Open Access

    Methods for dilation are currently limited to specific shapes and curvatures, with the potential for some of the structure's shape to encroach onto the final dilated volume. Here, the authors develop a method for creating dilational structures from arbitrary surfaces that avoids volume encroachment.

    • Freek G. J. Broeren
    • , Werner W. P. J. van de Sande
    • , Volkert van der Wijk
    •  & Just L. Herder
  • Article
    | Open Access

    The spatial structure of a population is often critical for the evolution of cooperation. Here, Allen and colleagues show that when spatial structure is represented by an isothermal graph, the effective number of neighbors per individual determines whether or not cooperation can evolve.

    • Benjamin Allen
    • , Gabor Lippner
    •  & Martin A. Nowak
  • Article
    | Open Access

    Theories state that transitions between extreme waves are allowed but experimental confirmations are lacking because of lack of control strategies. Here, the authors propose and experimentally report, for the first time, the use of topological indices to control the generation of extreme waves.

    • Giulia Marcucci
    • , Davide Pierangeli
    • , Aharon J. Agranat
    • , Ray-Kuang Lee
    • , Eugenio DelRe
    •  & Claudio Conti
  • Article
    | Open Access

    Is there an optimum difficulty level for training? In this paper, the authors show that for the widely-used class of stochastic gradient-descent based learning algorithms, learning is fastest when the accuracy during training is 85%.

    • Robert C. Wilson
    • , Amitai Shenhav
    • , Mark Straccia
    •  & Jonathan D. Cohen
  • Article
    | Open Access

    Transcript assembly is an important step in analysis of RNA-seq data whose accuracy influences downstream quantification, detection and characterization of alternative splice variants. Here, the authors develop PsiCLASS, a transcript assembler leveraging simultaneous analysis of multiple RNA-seq samples.

    • Li Song
    • , Sarven Sabunciyan
    • , Guangyu Yang
    •  & Liliana Florea
  • Article
    | Open Access

    The use of single-photon data has been limited by time-consuming reconstruction algorithms. Here, the authors combine statistical models and computational tools known from computer graphics and show real-time reconstruction of moving scenes.

    • Julián Tachella
    • , Yoann Altmann
    • , Nicolas Mellado
    • , Aongus McCarthy
    • , Rachael Tobin
    • , Gerald S. Buller
    • , Jean-Yves Tourneret
    •  & Stephen McLaughlin
  • Article
    | Open Access

    The brain can often continue to function despite lesions in many areas, but damage to particular locations may have serious effects. Here, the authors use the concept of Ollivier-Ricci curvature to investigate the robustness of brain networks.

    • Hamza Farooq
    • , Yongxin Chen
    • , Tryphon T. Georgiou
    • , Allen Tannenbaum
    •  & Christophe Lenglet
  • Article
    | Open Access

    Discovery of hybrid dynamical models for real-world cyber-physical systems remains a challenge. This paper proposes a general framework for automating mechanistic modeling of hybrid dynamical systems from observed data with low computational complexity and noise resilience.

    • Ye Yuan
    • , Xiuchuan Tang
    • , Wei Zhou
    • , Wei Pan
    • , Xiuting Li
    • , Hai-Tao Zhang
    • , Han Ding
    •  & Jorge Goncalves
  • Article
    | Open Access

    Viral assembly is a complex process that in tailed bacteriophages involves scaffolding proteins which coordinate assembly of the phage procapsid and are subsequently released during maturation. Here the authors reveal the conformational changes that accompany virion maturation, documenting how the dissociation of scaffold proteins and DNA packaging processes intersect.

    • Athanasios Ignatiou
    • , Sandrine Brasilès
    • , Mehdi El Sadek Fadel
    • , Jörg Bürger
    • , Thorsten Mielke
    • , Maya Topf
    • , Paulo Tavares
    •  & Elena V. Orlova
  • Article
    | Open Access

    Natural creatures, from fish to snake and birds, combine neural control, sensory feedback and compliant mechanics to operate across uncertain environments. Here the authors present a versatile modeling approach to the dynamic simulation of their architectures based on the assembly of Cosserat rods.

    • Xiaotian Zhang
    • , Fan Kiat Chan
    • , Tejaswin Parthasarathy
    •  & Mattia Gazzola
  • Article
    | Open Access

    The scale and dimensionality of imaging data means information is commonly overlooked. Here, using recurrent neural networks we understand temporal dependencies in hyperspectral imagery, enabling the observation of differences in ferroelectric switching mechanisms in PbZr0.2Ti0.8O3 thin films due to formation of charged domain walls.

    • Joshua C. Agar
    • , Brett Naul
    • , Shishir Pandya
    • , Stefan van der Walt
    • , Joshua Maher
    • , Yao Ren
    • , Long-Qing Chen
    • , Sergei V. Kalinin
    • , Rama K. Vasudevan
    • , Ye Cao
    • , Joshua S. Bloom
    •  & Lane W. Martin
  • Article
    | Open Access

    The extent to which brain structure and function are coupled remains a complex question. Here, the authors show that coupling strength between structural connectivity and functional activity can be quantified and reveals a cortical gradient spanning from lower-level sensory areas to high-level cognitive ones.

    • Maria Giulia Preti
    •  & Dimitri Van De Ville
  • Article
    | Open Access

    Though conductivity doping in organic semiconductors has been widely studied in organic electronics, a clear mechanistic picture that explains the phenomenon is still lacking. Here, the authors report a theoretical approach to elucidate the role of disorder compensation in doped organic materials.

    • Artem Fediai
    • , Franz Symalla
    • , Pascal Friederich
    •  & Wolfgang Wenzel
  • Article
    | Open Access

    The inverse DFT problem of mapping the ground-state density to its exchange correlation potential has been numerically challenging so far. Here, the authors propose an approach for an accurate solution to the inverse DFT problem, enabling the evaluation of exact exchange and correlation potential from an ab initio density.

    • Bikash Kanungo
    • , Paul M. Zimmerman
    •  & Vikram Gavini
  • Article
    | Open Access

    Viruses have evolved protein containers with a wide spectrum of icosahedral architectures but the geometric constraints defining these container designs remain to be understood. Here authors revisit the construction of icosahedral architectures using the Archimedean lattices that explain the outliers to the current classification scheme.

    • Reidun Twarock
    •  & Antoni Luque
  • Article
    | Open Access

    The increasing accessibility of single cell RNA sequencing demands tools that enable data visualization and interpretation. Here, the authors introduce Vision, a flexible annotation tool that operates directly on the manifold of cell-cell similarity and aids interpretation of cellular heterogeneity.

    • David DeTomaso
    • , Matthew G. Jones
    • , Meena Subramaniam
    • , Tal Ashuach
    • , Chun J. Ye
    •  & Nir Yosef
  • Article
    | Open Access

    Neural signalling is directional, but non-invasive neuroimaging methods are unable to map directed connections between brain regions. Here, the authors show how network communication measures can be used to infer signalling directionality from the undirected topology of brain structural connectomes.

    • Caio Seguin
    • , Adeel Razi
    •  & Andrew Zalesky
  • Article
    | Open Access

    HiChIP/PLAC-seq assay is popular for profiling 3D genome interactions among regulatory elements at kilobase resolution. Here the authors describe FitHiChIP an empirical null-based, flexible computational method for statistical significance estimation and loop calling from HiChIP data.

    • Sourya Bhattacharyya
    • , Vivek Chandra
    • , Pandurangan Vijayanand
    •  & Ferhat Ay
  • Article
    | Open Access

    The hidden matching communication problem features an exponential classical-quantum gap, but a demonstration is extremely challenging. Here, the authors define a more feasible variant called sampling matching problem, and realise a proof-of-principle implementation beating the best known classical protocol.

    • Niraj Kumar
    • , Iordanis Kerenidis
    •  & Eleni Diamanti
  • Article
    | Open Access

    We currently lack generic methods to map RNA modifications across the entire transcriptome. Here, the authors demonstrate that m6A RNA modifications can be detected with high accuracy using nanopore direct RNA sequencing.

    • Huanle Liu
    • , Oguzhan Begik
    • , Morghan C. Lucas
    • , Jose Miguel Ramirez
    • , Christopher E. Mason
    • , David Wiener
    • , Schraga Schwartz
    • , John S. Mattick
    • , Martin A. Smith
    •  & Eva Maria Novoa
  • Article
    | Open Access

    The relationship between metabolomic and behavioral changes is not well understood. Here, the authors analyze metabolome changes in D. melanogaster heads and bodies during hunger and satiety, and develop the Flyscape tool to visualize the resulting metabolic networks and integrate them with other omics data.

    • Daniel Wilinski
    • , Jasmine Winzeler
    • , William Duren
    • , Jenna L. Persons
    • , Kristina J. Holme
    • , Johan Mosquera
    • , Morteza Khabiri
    • , Jason M. Kinchen
    • , Peter L. Freddolino
    • , Alla Karnovsky
    •  & Monica Dus
  • Article
    | Open Access

    Forecasting aftershock earthquakes is a critical step in improving seismic hazard mitigation. The authors here combine Bayesian methods with extreme value theory to tackle this problem - and manage to estimate the maximum magnitude of an expected earthquake as well as the arrival times in a pre-defined window.

    • Robert Shcherbakov
    • , Jiancang Zhuang
    • , Gert Zöller
    •  & Yosihiko Ogata
  • Article
    | Open Access

    When a viscous fluid is displaced by a less viscous phase between two plates, a finger-like instability occurs. Here the authors demonstrate how applying an external electric field can suppress the fingering instability without the need to alter the fluid flow rate or the gap geometry.

    • Tao Gao
    • , Mohammad Mirzadeh
    • , Peng Bai
    • , Kameron M. Conforti
    •  & Martin Z. Bazant
  • Article
    | Open Access

    Systematic methods to characterize human mobility can lead to more accurate forecasting of epidemic spreading and better urban planning. Here the authors present a methodology to analyse daily commuting data by representing it with an irrotational vector field and a corresponding scalar potential.

    • Mattia Mazzoli
    • , Alex Molas
    • , Aleix Bassolas
    • , Maxime Lenormand
    • , Pere Colet
    •  & José J. Ramasco
  • Article
    | Open Access

    Primary visual cortical neurons exhibit diverse responses to visual stimuli yet how these signals are integrated during visual perception is not well understood. Here, the authors show that optogenetic stimulation of neurons situated near the visually‐driven population leads to improved orientation detection in monkeys through changes in correlated variability.

    • Ariana R. Andrei
    • , Sorin Pojoga
    • , Roger Janz
    •  & Valentin Dragoi
  • Perspective
    | Open Access

    Recent gains in artificial neural networks rely heavily on large amounts of training data. Here, the author suggests that for AI to learn from animal brains, it is important to consider that animal behaviour results from brain connectivity specified in the genome through evolution, and not due to unique learning algorithms.

    • Anthony M. Zador
  • Article
    | Open Access

    The role of climate change (CC) contrarians is neglected in climate change communication studies. Here the authors used a data-driven approach to identify CC contrarians and CC scientists and found that CC scientists have much higher citation impact than those for contrarians but lower media visibility.

    • Alexander Michael Petersen
    • , Emmanuel M. Vincent
    •  & Anthony LeRoy Westerling
  • Article
    | Open Access

    Oral care based foods are of great interest for increasing the dental health of animals. Here, the authors report on computer simulations to optimise the texture and geometry of food in order to maximise tooth abrasion and enhance cleaning efficiency.

    • C. G. Skamniotis
    • , M. Elliott
    •  & M. N. Charalambides
  • Article
    | Open Access

    Plasmodesmata channels connect neighbouring plant cells and respond to external stimuli via changes in permeability. Here Park et al. propose that mechanical forces can displace the dumbbell-shaped ER-desmotubule complex that spans the central plasmodesmatal cylinder leading to closure of the pore.

    • Keunhwan Park
    • , Jan Knoblauch
    • , Karl Oparka
    •  & Kaare H. Jensen
  • Article
    | Open Access

    There is a lack of systematic approaches to identify and analyze the hierarchical structure of geo-industrial clusters at the global scale. Here the authors use LinkedIn's employment history data to construct a global labor flow network from which they find that the resulting geo-industrial clusters exhibit a stronger association between the influx of educated-workers and financial performance compared to existing aggregation units.

    • Jaehyuk Park
    • , Ian B. Wood
    • , Elise Jing
    • , Azadeh Nematzadeh
    • , Souvik Ghosh
    • , Michael D. Conover
    •  & Yong-Yeol Ahn
  • Article
    | Open Access

    The identification of cross-linked peptides at a proteome scale for interactome analyses represents a complex challenge. Here the authors report an efficient and reliable search engine pLink 2 for proteome-scale cross-linking mass spectrometry analyses, and demonstrate how to systematically evaluate the credibility of search engines.

    • Zhen-Lin Chen
    • , Jia-Ming Meng
    • , Yong Cao
    • , Ji-Li Yin
    • , Run-Qian Fang
    • , Sheng-Bo Fan
    • , Chao Liu
    • , Wen-Feng Zeng
    • , Yue-He Ding
    • , Dan Tan
    • , Long Wu
    • , Wen-Jing Zhou
    • , Hao Chi
    • , Rui-Xiang Sun
    • , Meng-Qiu Dong
    •  & Si-Min He
  • Article
    | Open Access

    The position, shape and number of transcription start sites (TSS) regulate gene expression. Here authors present MAPCap, a method for high-resolution detection and differential expression analysis of TSS, and apply MAPCap to early fly development, detecting stage and sex-specific promoter and enhancer activity.

    • Vivek Bhardwaj
    • , Giuseppe Semplicio
    • , Niyazi Umut Erdogdu
    • , Thomas Manke
    •  & Asifa Akhtar
  • Article
    | Open Access

    Designing alternative paradigms for bio-inspired analog computing that harnesses collective dynamics remains a challenge. Here, the authors exploit the synchronization dynamics of coupled vanadium dioxide-based insulator-to-metal phase-transition nano-oscillators for adaptive locomotion control.

    • Sourav Dutta
    • , Abhinav Parihar
    • , Abhishek Khanna
    • , Jorge Gomez
    • , Wriddhi Chakraborty
    • , Matthew Jerry
    • , Benjamin Grisafe
    • , Arijit Raychowdhury
    •  & Suman Datta
  • Article
    | Open Access

    Anonymization has been the main means of addressing privacy concerns in sharing medical and socio-demographic data. Here, the authors estimate the likelihood that a specific person can be re-identified in heavily incomplete datasets, casting doubt on the adequacy of current anonymization practices.

    • Luc Rocher
    • , Julien M. Hendrickx
    •  & Yves-Alexandre de Montjoye
  • Article
    | Open Access

    Approaches to examine the urbanization impact on climate change ignore that interactions between size and density may have an important influence on urban emissions. Here the authors show that variations in the emissions associated with changes in population or density may not only depend on the magnitude of these changes but also on the initial values of these quantities.

    • Haroldo V. Ribeiro
    • , Diego Rybski
    •  & Jürgen P. Kropp