508 Works

Data from: Dietary choices are influenced by genotype, mating status, and sex in Drosophila melanogaster

M. Florencia Camus, Chun-Chen Huang, Max Reuter, Kevin Fowler & Chun-Cheng Huang
Mating causes many changes in physiology, behaviour and gene expression in a wide range of organisms. These changes are predicted to be sex-specific, influenced by the divergent reproductive roles of the sexes. In female insects, mating is associated with an increase in egg production which requires high levels of nutritional input with direct consequences for the physiological needs of individual females. Consequently, females alter their nutritional acquisition in line with the physiological demands imposed by...

Data from: Sporadic sampling not climatic forcing drives observed early hominin diversity

Simon J. Maxwell, Philip J. Hopley, Paul Upchurch & Christophe Soligo
The role of climate change in the origin and diversification of early hominins is hotly debated. Most accounts of early hominin evolution link observed fluctuations in species diversity to directional shifts in climate or periods of intense climatic instability. None of these hypotheses, however, have tested whether observed diversity patterns are distorted by variation in the quality of the hominin fossil record. Here, we present a detailed examination of early hominin diversity dynamics, including both...

Data from: Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?

Irepan Salvador-Martínez, Marco Grillo, Michalis Averof & Maximilian J. Telford
Cell lineages provide the framework for understanding how multicellular organisms are built and how cell fates are decided during development. Describing cell lineages in most organisms is challenging, given the number of cells involved; even a fruit fly larva has ~50,000 cells and a small mammal has more than 1 billion cells. Recently, the idea of using CRISPR to induce mutations during development as heritable markers for lineage reconstruction has been proposed and trialled by...

Data from: Decision and navigation in mouse parietal cortex

Michael Krumin, Julie J. Lee, Kenneth D. Harris & Matteo Carandini
Posterior parietal cortex (PPC) has been implicated in navigation, in the control of movement, and in visually-guided decisions. To relate these views, we measured activity in PPC while mice performed a virtual navigation task driven by visual decisions. PPC neurons were selective for specific combinations of the animal's spatial position and heading angle. This selectivity closely predicted both the activity of individual PPC neurons, and the arrangement of their collective firing patterns in choice-selective sequences....

Data from: Non-invasive imaging of CSF-mediated brain clearance pathways via assessment of perivascular fluid movement with DTI MRI

Ian F. Harrison, Bernard Siow, Aisha B. Akilo, Phoebe G. Evans, Ozama Ismail, Yolanda Ohene, Payam Nahavandi, David L. Thomas, Mark F. Lythgoe & Jack A. Wells
The glymphatics system describes a CSF-mediated clearance pathway for the removal of potentially harmful molecules, such as amyloid beta, from the brain. As such, its components may represent new therapeutic targets to alleviate aberrant protein accumulation that defines the most prevalent neurodegenerative conditions. Currently, however, the absence of any non-invasive measurement technique prohibits detailed understanding of glymphatic function in the human brain and in turn, it's role in pathology. Here, we present the first non-invasive...

Data from: An assessment of the role of the falx cerebri and tentorium cerebelli in the cranium of the cat (Felis silvestris catus)

Víctor Sellés De Lucas, Hugo Dutel, Susan E. Evans, Flora Gröning, Alana C. Sharp, Peter J. Watson & Michael J. Fagan
The falx cerebri and the tentorium cerebelli are two projections of the dura mater in the cranial cavity which ossify to varying degrees in some mammalian species. The idea that the ossification of these structures may be necessary to support the loads arising during feeding has been proposed and dismissed in the past, but never tested quantitatively. To address this, a biomechanical model of a domestic cat (Felis silvestris catus) skull was created and the...

Phase resolution of heterozygous sites in diploid genomes is important to phylogenomic analysis under the multispecies coalescent model

Ziheng Yang, Jun Huang, Tomas Flouri, Jeremy Bennett & Adam Leache
Genome sequencing projects routinely generate haploid consensus sequences from diploid genomes, which are effectively chimeric sequences with the phase at heterozygous sites resolved at random. The impact of phasing errors on phylogenomic analyses under the multispecies coalescent (MSC) model is largely unknown. Here we conduct a computer simulation to evaluate the performance of four phase-resolution strategies (the true phase resolution, the diploid analytical integration algorithm which averages over all phase resolutions, computational phase resolution using...

Data package from 'Pantropical variability in tree crown allometry' Global Ecology and Biogeography 2021. DOI: 10.1111/geb.13231

Grace Jopaul Loubota Panzou, Adeline Fayolle, Tommaso Jucker, Oliver Phillips, Stephanie Bohlman, Lindsay F. Banin, Simon L. Lewis, Kofi Affum-Baffoe, Luciana F. Alves, Cécile Antin, Eric Arets, Luzmila Arroyo, Timothy R. Baker, Nicolas Barbier, Hans Beeckman, Uta Berger, Yannick Enock Bocko, Frans Bongers, Sam Bowers, Thom Brade, Eduardo S. Brondizio, Arthur Chantrain, Jerome Chave, Halidou Compaore & David Coomes

Coexistence of predators in time: effects of season and prey availability on species activity within a Mediterranean carnivore guild

Marc Vilella, Mariona Ferrandiz-Rovira & Ferran Sayol
1. The degree of coexistence among predators can determine the structure of ecological communities. Niche partitioning is a common strategy applied by species to enhance their coexistence. Diet, habitat or time use can be responsible for segregation among carnivore species, the latter factor being the least studied in Mediterranean ecosystems. Terrestrial medium-sized carnivores (i.e. mesocarnivores) carry out important functions in ecosystems and identifying their interactions is essential for their conservation. 2. In this study, we...

The asymptotic behavior of bootstrap support values in molecular phylogenetics

Jun Huang, Yuting Liu, Tianqi Zhu & Ziheng Yang
The phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML). It is observed that bootstrap support tends to be high in large genomic datasets whether or not the inferred trees and clades are correct. Here we study the asymptotic behavior of bootstrap support for the ML tree in large datasets when the competing phylogenetic trees are equally right...

Data from: Meiotic drive does not cause condition-dependent reduction of the sexual ornament in stalk-eyed flies

Sam Finnegan, Matteo Mondani, Kevin Fowler & Andrew Pomiankowski
Meiotic drive systems are associated with low frequency chromosomal inversions. These are expected to accumulate deleterious mutations due to reduced recombination and low effective population size. We test this prediction using the “sex-ratio” (SR) meiotic drive system of the Malaysian stalk-eyed fly Teleopsis dalmanni.SR is associated with a large inversion (or inversions) on the X chromosome. In particular, we study eyespan in males carrying the SR chromosome, as this trait is a highly exaggerated, sexually...

Cerebral small vessel disease and functional outcome prediction after intracerebral haemorrhage

David Werring, Ghil Schwarz & Isabel Hostettler
Background. It is unknown whether adding cerebral small vessel disease (SVD) biomarkers can improve the performance of intracerebral hemorrhage (ICH) outcome predictive scores. Purpose. To determine whether: (1) CT-based SVD biomarkers are associated with 6-month functional outcome after ICH and (2) whether these biomarkers improve the performance of pre-existing ICH score. Methods. We included 864 patients with acute ICH from a multicentre, hospital-based prospective cohort study. We evaluated CT-based SVD biomarkers (white matter hypodensities [WMH];...

Spatial modulation of visual responses arises in cortex with active navigation

, Charu Bai Reddy, Sylvia Schröder, Tomaso Muzzu, Kenneth D. Harris, Aman B. Saleem & Matteo Carandini
During navigation, the visual responses of neurons in mouse primary visual cortex (V1) are modulated by the animal’s spatial position. Here we show that this spatial modulation is similarly present across multiple higher visual areas but negligible in the main thalamic pathway into V1. Similar to hippocampus, spatial modulation in visual cortex strengthens with experience and with active behavior. Active navigation in a familiar environment, therefore, enhances the spatial modulation of visual signals starting in...

Sudden Unexpected Death in Epilepsy: A Personalized Prediction Tool

Ashwani Jha, Cheongeun Oh, Dale Hesdorffer, Beate Diehl, Sasha Devore, Martin Brodie, Torbjörn Tomson, Josemir W. Sander, Thaddeus S. Walczak & Orrin Devinsky
Objective: To develop and validate a tool for individualised prediction of Sudden Unexpected Death in Epilepsy (SUDEP) risk, we re-analysed data from one cohort and three case-control studies undertaken 1980-2005. Methods: We entered 1273 epilepsy cases (287 SUDEP, 986 controls) and 22 clinical predictor variables into a Bayesian logistic regression model. Results: Cross-validated individualized model predictions were superior to baseline models developed from only average population risk or from generalised tonic-clonic seizure frequency (pairwise difference...

Historical analysis of seagrass loss in the United Kingdom

Alix E. Green, Michael A. Chadwick, Richard K.F. Unsworth & Peter J.S. Jones
This dataset includes empirical and qualitative data from a multitude of sources using systematic review methods to provide analysis on seagrass occurrence and loss in the United Kingdom. We document 8,493 ha of recently mapped seagrass in the UK since 1998.

Data associated with: Going round the twist – An empirical analysis of shell coiling in helicospiral gastropods

Katie S. Collins, Roman Klapaukh, James S. Crampton, Michael F. Gazley, C. Ian Schipper, Anton Maksimenko & Benjamin R. Hines
The logarithmic helicospiral has been the most widely accepted model of regularly coiled mollusc form since it was proposed by Moseley (1838) and popularised by Thompson (1942) and Raup (1966). It is based on an explicit assumption that shells are isometric and grow exponentially, and an implicit assumption that the external form of the shell follows the internal shape, which implies that the parameters of the spiral could, theoretically, be reconstructed from the external whorl...

Breaking a species barrier by enabling hybrid recombination

G. Ozan Bozdag, Jasmine Ono, Jai A. Denton, Emre Karakoc, Neil Hunter, Jun-Yi Leu & Duncan Greig
Hybrid sterility maintains reproductive isolation between species by preventing them from exchanging genetic material. Anti-recombination can contribute to hybrid sterility when different species’ chromosome sequences are too diverged to cross-over efficiently during hybrid meiosis, resulting in chromosome mis-segregation and aneuploidy. The genome sequences of the yeasts Saccharomyces cerevisiae and Saccharomyces paradoxus have diverged by about 12% and their hybrids are sexually sterile: nearly all of their gametes are aneuploid and inviable. Previous methods to increase...

Middle Eocene terrestrial paleoweathering and climate evolution in the midlatitude Bohai Bay Basin of Eastern China

Di Chen, Xiongqi Pang, Kun Zhang, Guoyong Liu, Fujie Jiang, Liang Li, Youwei Wang, Min Li & Yang Liu
The middle Eocene is a key time period for understanding Cenozoic cooling of the global climate. In eastern Asia, this time period was marked by deposition of extensive mudstones, shales and interbedded siltstones, especially in the midlatitude Bohai Bay Basin. Still, midlatitude terrestrial records of climate evolution during the middle Eocene are rare. Here, we analyze a continuous, high-resolution record of this period using samples of the shales in the fourth submember of the third...

Natural history, phenotypic spectrum, and discriminative features of multisystemic RFC1-disease

Andreas Traschütz, Andrea Cortese, Selina Reich, Natalia Dominik, Jennifer Faber, Heike Jacobi, Annette Hartmann, Dan Rujescu, Solveig Montaut, Andoni Echaniz-Laguna, Sevda Erer, Valerie Cornelia Schütz, Alexander Tarnutzer, Marc Sturm, Tobias Haack, Nadège Vaucamps-Diedhiou, Helene Puccio, Ludger Schöls, Thomas Klockgether, Bart P. Van De Warrenburg, Martin Paucar, Dagmar Timmann, Ralf-Dieter Hilgers, Jose Gazulla, Michael Strupp … & Matthis Synofzik
Objective: To delineate the full phenotypic spectrum, discriminative features, piloting longitudinal progression data, and sample size calculations of RFC1-repeat expansions, recently identified as causing cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS). Methods: Multimodal RFC1 repeat screening (PCR, southern blot, whole-exome/genome (WES/WGS)-based approaches) combined with cross-sectional and longitudinal deep-phenotyping in (i) cross-European cohort A (70 families) with ≥2 features of CANVAS and/or ataxia-with-chronic-cough (ACC); and (ii) Turkish cohort B (105 families) with unselected late-onset ataxia. Results:...

A non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster exhibits antagonistically pleiotropic fitness effects

Michael Jardine, Filip Ruzicka, Charlotte Diffley, Kevin Fowler & Max Reuter
The amount of genetic variation for fitness within populations tends to exceed that expected under mutation-selection-drift balance. Several mechanisms have been proposed to actively maintain polymorphism and account for this discrepancy, including antagonistic pleiotropy (AP), where allelic variants have opposing effects on different components of fitness. Here we identify a non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster and measure survival and reproductive components of fitness in males and females of replicate lines...

Borane Catalyzed Stereoselective C–H insertion, Cyclopropanation, and Ring-Opening Reactions - data

Ayan Dasgupta, Rasool Babaahmadi, Ben Slater, Brian F Yates, Alireza Ariafard & Rebecca L Melen
Lewis acidic boranes have been shown to be an effective metal-free catalyst for highly selective reactions of donor-acceptor diazo compounds to a range of substrates. The reactions of α-aryl α-diazoesters with nitrogen heterocycles indole or pyrrole selectively generates C3 and C2 C–H insertion products respectively in good to excellent yields even when using unprotected indoles. Alternatively, benzofuran, indene, and alkene substrates give exclusively cyclopropanated products with α-aryl α-diazoesters, whereas the reactions with furans leads to...

HemeLB input files for areteriovenous fistula simulation

Peter Coveney & Jon McCullough
This dataset contains the HemeLB input files used to run the blood flow simulations described in our manuscript "High fidelity physiological blood flow in patient-specific arteriovenous fistula for clinical applications". These work with the PressureCouplingBeds and ResistorCapacitorBeds branches of the source code available at https://github.com/UCL-CCS/HemePure_SelfCoupled. Provided in this dataset are four *.tar.gz files containing the necessary input files for the flow simulations through the arteries and veins of the left forearm discussed in our manuscript:...

Flow cytometry data: healthy donor bone marrow taken during hip surgery

Jessica Timms, James Opzoomer, Kevin Blighe, Thanos Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca Ciccarelli, Peter Parker, Michaela Fontenay, Paul Barber, James Arnold & Shahram Kordasti
High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster) an R package for immune profiling cellular heterogeneity in high dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by...

Imaging mass cytometry data: Diffuse large B-cell lymphoma lymph node section

Jessica Timms, James Opzoomer, Kevin Blighe, Thanos Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca Ciccarelli, Peter Parker, Michaela Fontenay, Paul Barber, James Arnold & Shahram Kordasti
High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster) an R package for immune profiling cellular heterogeneity in high dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by...

Improving assessments of data-limited populations using life-history theory

Cat Horswill, Andrea Manica, Francis Daunt, Mark Newell, Sarah Wanless, Matthew Wood & Jason Matthiopoulos
1. Predicting how populations may respond to climate change and anthropogenic pressures requires detailed knowledge of demographic traits, such as survival and reproduction. However, the availability of these data varies greatly across space and taxa. Therefore, it is common practice to conduct population assessments by filling in missing values from surrogate species or other populations of the same species. Using these independent surrogate values concurrently with observed data neglects the life‐history trade‐offs that connect the...

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