bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using activity and sociability to characterize collective motion
Authors: Sumpter David J. T. , Szorkovszky Alex , Kotrschal Alexander , Kolm Niclas , Herbert-Read James E. 
Published: March 2018

A wide range of measurements can be made on the collective motion of groups, and the movement of individuals within them. These include, but are not limited to: group size, polarization, speed, turning speed, speed or directional correlations, and distances to near neighbours. From an ecological and evolutionary perspective, we would like to know which of these measurements capture biologically meaningful aspects of an animal's behaviour and contribute to its survival chances. Previous simulation studies have emphasized two main factors shaping individuals' behaviour in groups; attraction and alignment. Alignment responses appear to be important in transferring information between group members and providing synergistic benefits to group members. Likewise, attraction to conspecifics is thought to provide benefits through, for example, selfish herding. Here, we use a factor analysis on a wide range of simple measurements to identify two main axes of collective motion in guppies (Poecilia reticulata): (i) sociability, which corresponds to attraction (and to a lesser degree alignment) to neighbours, and (ii) activity, which combines alignment with directed movement. We show that for guppies, predation in a natural environment produces higher degrees of sociability and (in females) lower degrees of activity, while female guppies sorted for higher degrees of collective alignment have higher degrees of both sociability and activity. We suggest that the activity and sociability axes provide a useful framework for measuring the behaviour of animals in groups, allowing the comparison of individual and collective behaviours within and between species.This article is part of the theme issue ‘Collective movement ecology’.
Eco-evolutionary dynamics, density-dependent dispersal and collective behaviour: implications for salmon metapopulation robustness
Authors: Yeakel Justin D. , Gibert Jean P. , Gross Thilo , Westley Peter A. H. , Moore Jonathan W. 
Published: March 2018

The spatial dispersal of individuals plays an important role in the dynamics of populations, and is central to metapopulation theory. Dispersal provides connections within metapopulations, promoting demographic and evolutionary rescue, but may also introduce maladapted individuals, potentially lowering the fitness of recipient populations through introgression of heritable traits. To explore this dual nature of dispersal, we modify a well-established eco-evolutionary model of two locally adapted populations and their associated mean trait values, to examine recruiting salmon populations that are connected by density-dependent dispersal, consistent with collective migratory behaviour that promotes navigation. When the strength of collective behaviour is weak such that straying is effectively constant, we show that a low level of straying is associated with the highest gains in metapopulation robustness and that high straying serves to erode robustness. Moreover, we find that as the strength of collective behaviour increases, metapopulation robustness is enhanced, but this relationship depends on the rate at which individuals stray. Specifically, strong collective behaviour increases the presence of hidden low-density basins of attraction, which may serve to trap disturbed populations, and this is exacerbated by increased habitat heterogeneity. Taken as a whole, our findings suggest that density-dependent straying and collective migratory behaviour may help metapopulations, such as in salmon, thrive in dynamic landscapes. Given the pervasive eco-evolutionary impacts of dispersal on metapopulations, these findings have important ramifications for the conservation of salmon metapopulations facing both natural and anthropogenic contemporary disturbances.This article is part of the theme issue ‘Collective movement ecology’.
Inferring the rules of social interaction in migrating caribou
Authors: Torney Colin J. , Lamont Myles , Debell Leon , Angohiatok Ryan J. , Leclerc Lisa-Marie , Berdahl Andrew M. 
Published: March 2018

Social interactions are a significant factor that influence the decision-making of species ranging from humans to bacteria. In the context of animal migration, social interactions may lead to improved decision-making, greater ability to respond to environmental cues, and the cultural transmission of optimal routes. Despite their significance, the precise nature of social interactions in migrating species remains largely unknown. Here we deploy unmanned aerial systems to collect aerial footage of caribou as they undertake their migration from Victoria Island to mainland Canada. Through a Bayesian analysis of trajectories we reveal the fine-scale interaction rules of migrating caribou and show they are attracted to one another and copy directional choices of neighbours, but do not interact through clearly defined metric or topological interaction ranges. By explicitly considering the role of social information on movement decisions we construct a map of near neighbour influence that quantifies the nature of information flow in these herds. These results will inform more realistic, mechanism-based models of migration in caribou and other social ungulates, leading to better predictions of spatial use patterns and responses to changing environmental conditions. Moreover, we anticipate that the protocol we developed here will be broadly applicable to study social behaviour in a wide range of migratory and non-migratory taxa.
This article is part of the theme issue ‘Collective movement ecology’.
Linear-double-stranded DNA (ldsDNA) based AND logic computation in mammalian cells
Authors: Su Weijun , Zhang Chunze , Li Shuai 
Published: March 2018

AbstractSynthetic biology employs engineering principles to redesign biological system for clinical or industrial purposes. The development and application of novel genetic devices for genetic circuits construction will facilitate the rapid development of synthetic biology. Here we demonstrate that mammalian cells could perform two- and three-input linear-double-stranded DNA (ldsDNA) based Boolean AND logic computation. Through hydrodynamic ldsDNA delivery, two-input ldsDNA-base AND-gate computation could be achieved in vivo. Inhibition of DNA-PKcs expression, a key enzyme in non-homologous end joining (NHEJ), could significantly downregulate the intensity of output signals from ldsDNA-based AND-gate. We further reveal that in mammalian cells ldsDNAs could undergo end processing and then perform AND-gate calculation to generate in-frame output proteins. Moreover, we show that ldsDNAs or plasmids with identical overlapping sequences could also serve as inputs of AND-gate computation. Our work establishes novel genetic devices and principles for genetic circuits construction, thus may open a new gate for the development of new disease targeting strategies and new protein genesis methodologies.
High-accuracy Decoding of Complex Visual Scenes from Neuronal Calcium Responses
Authors: Ellis Randall J. , Michaelides Michael 
Published: March 2018

AbstractThe brain contains billions of neurons defined by diverse cytoarchitectural, anatomical, genetic, and functional properties. Sensory encoding and decoding are popular research areas in the fields of neuroscience, neuroprosthetics and artificial intelligence but the contribution of neuronal diversity to these processes is not well understood. Deciphering this contribution necessitates development of sophisticated neurotechnologies that can monitor brain physiology and behavior via simultaneous assessment of individual genetically-defined neurons during the presentation of discrete sensory cues and behavioral contexts. Neural networks are a powerful technique for formulating hierarchical representations of data using layers of nonlinear transformations. Here we leverage the availability of an unprecedented collection of neuronal activity data, derived from ∼25,000 individual genetically-defined neurons of the parcellated mouse visual cortex during the presentation of 118 unique and complex naturalistic scenes, to demonstrate that neural networks can be used to decode discrete visual scenes from neuronal calcium responses with high (∼96%) accuracy. Our findings highlight the novel use of neural networks for sensory decoding using neuronal calcium imaging data and reveal a neuroanatomical map of visual decoding strength traversing brain regions, cortical layers, neuron types, and time. Our findings also demonstrate the utility of feature selection in assigning contributions of neuronal diversity to visual decoding accuracy and the low requirement of network architecture complexity for high accuracy decoding in this experimental context.
Causal mechanisms of a healthy lifestyle intervention for patients with musculoskeletal pain who are overweight or obese
Authors: Williams A , Lee H , Kamper SJ , O’Brien KM , Wiggers J , Wolfenden L , Yoong SL , Hodder RK , Robson EK , Haskins R , McAuley JH , Williams CM 
Published: March 2018

AbstractWe assessed the causal mechanisms of a healthy lifestyle intervention for patients with chronic low back pain and knee osteoarthritis (OA), who are overweight or obese. We conducted causal mediation analyses of aggregated data from two RCTs; which included 160 patients with chronic low back pain, and 120 patients with knee OA. Participants were randomised via one central randomisation schedule, to the intervention, or usual care. The intervention consisted of brief advice and referral to a 6-month telephone-based healthy lifestyle coaching service. Participants in the back pain trial were also offered a single physiotherapy consultation. The hypothesised primary mediator was self-reported weight, and alternative mediators were diet, physical activity, and pain beliefs. Outcomes were pain intensity, disability, and quality of life (QoL). Data were analysed using causal mediation analyses with sensitivity analyses for sequential ignorability. All mediation models were specified a priori. The intervention had no effect on pain intensity, disability or physical QoL. The intervention significantly improved mental QoL, however, the intervention effect was not channelled via the selected mediators. The intervention did not reduce weight, or the alternative mediators (diet, physical activity, pain beliefs), and these mediators were not associated with the outcomes (with one exception; poor diet was associated with lower mental QoL). The sensitivity analyses showed that our estimates were stable across all possible levels of residual confounding. Our findings show that the intervention did not cause a meaningful change in the hypothesised mediators, and these mediators were not associated with patient outcomes.
Sample size calculation for estimating key epidemiological parameters using serological data and mathematical modelling
Authors: Blaizot Stéphanie , Herzog Sereina A. , Abrams Steven , Theeten Heidi , Litzroth Amber , Hens Niel 
Published: March 2018

AbstractBackgroundOur work was motivated by the need to, given serum availability and/or financial resources, decide on which samples to test for different pathogens in a serum bank. Simulation-based sample size calculations were performed to determine the age-based sampling structures and optimal allocation of a given number of samples for testing across various age groups best suited to estimate key epidemiological parameters (e.g., seroprevalence or force of infection) with acceptable precision levels in a cross-sectional seroprevalence survey.MethodsStatistical and mathematical models and three age-based sampling structures (survey-based structure, population-based structure, uniform structure) were used. Our calculations are based on Belgian serological survey data collected in 2002 where testing was done, amongst others, for the presence of IgG antibodies against measles, mumps, and rubella, for which a national mass immunisation programme was introduced in 1985 in Belgium, and against varicella-zoster virus and parvovirus B19 for which the endemic equilibrium assumption is tenable in Belgium.ResultsThe optimal age-based sampling structure to use in the sampling of a serological survey as well as the optimal allocation distribution varied depending on the epidemiological parameter of interest for a given infection and between infections.ConclusionsWhen estimating key epidemiological parameters with acceptable levels of precision within the context of a single cross-sectional serological survey, attention should be given to the age-based sampling structure. Simulation-based sample size calculations in combination with mathematical modelling can be utilised for choosing the optimal allocation of a given number of samples over various age groups.
Thalamocortical And Intracortical Inputs Differentiate Layer-Specific Mouse Auditory Corticocollicular Neurons
Authors: Slater Bernard J. , Sons Stacy K. , Llano Daniel A. 
Published: March 2018

AbstractLong-range descending projections from the auditory cortex play key roles in shaping response properties in the inferior colliculus. The auditory corticocollicular projection is massive and heterogeneous, with axons emanating from cortical layers 5 and 6, and plays a key role in directing plastic changes in the inferior colliculus. However, little is known about the cortical and thalamic networks within which corticocollicular neurons are embedded. Here, laser scanning photostimulation glutamate uncaging and photoactivation of channelrhodopsin-2 were used to probe the local and long-range network differences between pre-identified mouse layer 5 and layer 6 auditory corticocollicular neurons in vitro. Layer 5 corticocollicular neurons were found to vertically integrate supragranular excitatory and inhibitory input to a substantially greater degree than their layer 6 counterparts. In addition, all layer 5 corticocollicular neurons received direct and large thalamic inputs from channelrhodopsin-2 labeled thalamocortical fibers whereas such inputs were less common in layer 6 corticocollicular neurons. Finally, a new low calcium/synaptic blockade approach to separate direct from indirect inputs using laser photostimulation was validated. These data demonstrate that layer 5 and 6 corticocollicular neurons receive distinct sets of cortical and thalamic inputs, supporting the hypothesis that they have divergent roles in modulating the inferior colliculus. Furthermore, the direct connection between the auditory thalamus and layer 5 corticocollicular neurons reveals a novel and rapid link connecting ascending and descending pathways.
Mapping malaria by combining parasite genomic and epidemiologic data
Authors: Wesolowski Amy , Taylor Aimee R. , Chang Hsiao-Han , Verity Robert , Tessema Sofonias , Bailey Jeffrey , Perkins T. Alex , Neafsey Daniel , Greenhouse Bryan , Buckee Caroline O. 
Published: March 2018

AbstractRecent global progress in scaling up malaria control interventions has revived the goal of complete elimination in many countries. Decreasing transmission intensity generally leads to increasingly patchy spatial patterns of malaria transmission, however, and control programs must accurately identify remaining foci in order to target interventions efficiently. In particular, mosquito control interventions like bed nets and insecticide spraying are best targeted to transmission hotspots, and the role of connectivity between different pockets of local transmission becomes increasingly important since humans are able to move parasites beyond the limits of mosquito dispersal and re-introduce parasites to previously malaria-free regions. Quantifying the connectivity between regions due to human travel, measuring malaria transmission intensity in different areas, and monitoring parasite spatial spread are therefore key issues for policy-makers because they underpin the feasibility of elimination and inform the path to its attainment. To this end, recent efforts have been made to develop new approaches to incorporating human mobility into spatial epidemiological models, for example using mobile phone data, and there has been a surge of interest in collecting spatially informative parasite samples to measure the genomic signatures of parasite connectivity. Due to their complicated life-cycles,Plasmodiumparasites pose unique challenges to researchers in this respect and new methods that move beyond traditional phylogenetic and population genetic tools must be developed to harness genetic information effectively. Here, we discuss the spatial epidemiology of malaria in the context of transmission-reduction interventions, and the challenges and promising directions for the development of integrated mapping, modeling, and genomic approaches that leverage disparate data sets to measure both connectivity and transmission.
A Generative Growth Model for Thalamocortical Axonal Branching in Primary Visual Cortex
Authors: Fard Pegah Kassraian , Pfeiffer Michael , Bauer Roman 
Published: March 2018

AbstractAxonal morphology displays large variability and complexity, yet the canonical regularities of the cortex suggest that such wiring is based on the repeated initiation of a small set of genetically encoded rules. Extracting underlying developmental principles can hence shed light on what genetically encoded instructions must be available during cortical development. Within a generative model, we investigate growth rules for axonal branching patterns in cat area 17, originating from the lateral geniculate nucleus of the thalamus. This target area of synaptic connections is characterized by extensive ramifications and a high bouton density, characteristics thought to preserve the spatial resolution of receptive fields and to enable connections for the ocular dominance columns. We compare individual and global statistics, such as a newly introduced asymmetry index and the global segment-length distribution, of generated and real branching patterns as the benchmark for growth rules. We show that the proposed model surpasses the statistical accuracy of the Galton-Watson model, which is the most commonly employed model for biological growth processes. In contrast to the Galton-Watson model, our model can recreate the log-normal segment-length distribution of the experimental dataset and is considerably more accurate in recreating individual axonal morphologies. To provide a biophysical interpretation for statistical quantifications of the axonal branching patterns, the generative model is ported into the physically accurate simulation framework of Cx3D. In this simulation environment we demonstrate how the proposed growth process can be formulated as an interactive process between genetic growth rules and chemical cues in the local environment.
PIP5k1 β controls bone homeostasis through modulating both osteoclast and osteoblast differentiation
Authors: Zhao Xiaoying , Hu Guoli , Wang Chuandong , Jiang Lei , Zhao Jingyu , Xu Jiake , Zhang Xiaoling 
Published: March 2018

AbstractPIP5K1β is crucial to generation of phosphotidylinosotol (4, 5) P2. PIP5K1β participates in numerous cellular activities, such as B cell and platelet activation, cell phagocytosis and endocytosis, cell apoptosis, and cytoskeletal organization. In the present work, we aimed to make insight into the function of PIP5K1β in osteoclastogenesis and osteogenesis to provide promising strategies for osteoporosis prevention and treatment. We discovered that PIP5k1β deletion in mice resulted in obvious bone loss and PIP5K1β was highly expressed both during osteoclast and osteoblast differentiation, besides, PIP5K1β deletion enhanced the proliferation and migration of BMMs to promote osteoclast differentiation. PIP5k1β−/−osteoclast exhibited normal cytoskeleton architecture but stronger resorption activity. PIP5k1β deficiency also promoted activation of MAPK and Akt signaling, enhanced TRAF6 and c-Fos expression, facilitated the expression and nuclear translocation of NFATC1 and upregulated Grb2 expression, thereby accelerating osteoclast differentiation and function. Finally, PIP5K1β enhanced osteoblast differentiation by upregulating master genes expression through triggering smad1/5/8 signaling. Thereby, PIP5K1β modulate bone homeostasis and remodeling.
Proof of concept for quantitative urine NMR metabolomics pipeline for large-scale epidemiology and genetics
Authors: Tynkkynen Tuulia , Wang Qin , Ekholm Jussi , Anufrieva Olga , Ohukainen Pauli , Vepsäläinen Jouko , Männikkö Minna , Keinänen-Kiukaanniemi Sirkka , Holmes Michael V. , Goodwin Matthew , Ring Susan , Chambers John C. , Kooner Jaspal , Järvelin Marjo-Riitta , Kettunen Johannes , Hill Michael , Smith George Davey , Ala-Korpela Mika 
Published: March 2018

AbstractBackgroundQuantitative molecular data from urine are rare in epidemiology and genetics. NMR spectroscopy could provide these data in high-throughput, and it has already been applied in epidemiological settings to analyse urine samples. However, quantitative protocols for large-scale applications are not available.MethodsWe describe in detail how to prepare urine samples and perform NMR experiments to obtain quantitative metabolic information. Semi-automated quantitative lineshape fitting analyses were set up for 43 metabolites and applied to data from various analytical test samples and from 1,004 individuals from a population-based epidemiological cohort. Novel analyses on how urine metabolites associate with quantitative serum NMR metabolomics data (61 metabolic measures; n=995) were performed. In addition, confirmatory genome-wide analyses of urine metabolites were conducted (n=578). The fully automated quantitative regression-based spectral analysis is demonstrated for creatinine and glucose (n= 4,548).ResultsIntra-assay metabolite variations were mostly <5% indicating high robustness and accuracy of the urine NMR spectroscopy methodology per se. Intra-individual metabolite variations were large, ranging from 6% to 194%. However, population-based inter-individual metabolite variations were even larger (from 14% to 1655%), providing a sound base for epidemiological applications. Metabolic associations between urine and serum were found clearly weaker than those within serum and within urine, indicating that urinary metabolomics data provide independent metabolic information. Two previous genome-wide hits for formate and 2-hydroxyisobutyrate were replicated at genome-wide significance.ConclusionsQuantitative urine metabolomics data suggest broad novelty for systems epidemiology. A roadmap for an open access methodology is provided.
Neuronal integration in the adult olfactory bulb is a non-selective addition process
Authors: Platel Jean-Claude , Angelova Alexandra , Bugeon Stephane , Ganay Thibault , Chudotvorova Ilona , Deloulme Jean-Christophe , Béclin Christophe , Tiveron Marie-Catherine , Coré Nathalie , Cremer Harold 
Published: March 2018

AbstractAdult neurogenesis is considered a competition in which neurons scramble during a critical period for integration and survival. Moreover, newborn neurons are thought to replace preexisting ones that die. Despite a wealth of evidence supporting this model, systematic in vivo observations of the process are still scarce. We used 2-photon imaging to study neuronal integration and survival directly in the olfactory bulb (OB) of living mice. Long-term tracking of over 1400 neurons demonstrated that cell-loss in the OB is virtually absent. Neuronal death resembling a critical period was induced by standard doses of BrdU or EdU, but disappeared when low doses of EdU were used, demonstrating toxicity. Finally, we demonstrate that the OB grows throughout life. This shows that neuronal selection during OB-neurogenesis does not occur during integration and argues against the existence of a critical period. Moreover, the OB is not a “turnover” system but shows lifelong neuronal addition.