Contributors: Ling, Hangjian, McIvor, Guillam, van der Vaart, Kasper, Vaughan, Richard, Thornton, Alex, Ouellette, Nicholas
... As one of nature’s most striking examples of collective behaviour, bird flocks have attracted extensive research. However, we still lack an understanding of the attractive and repulsive forces that govern interactions between individuals within flocks and how these forces influence neighbours’ relative positions and ultimately determine the shape of flocks. We address these issues by analysing the three-dimensional movements of wild jackdaws (Corvus monedula) in flocks containing 2 to 338 individuals. We quantify the social interaction forces in large, airborne flocks and find that these forces are highly anisotropic. The long-range attraction in the direction perpendicular to the movement direction is stronger than that along it, and the short-range repulsion is generated mainly by turning rather than changing speed. We explain this phenomenon by considering the wingbeat frequency and the change in the kinetic and gravitational potential energy during flight, and find that changing the direction of movement is less energetically costly than adjusting speed for birds. Furthermore, our data show that collision avoidance by turning can alter local neighbour distributions and ultimately change the group shape. Our results illustrate the macroscopic consequences of anisotropic interaction forces in bird flocks, and help to draw links between group structure, local interactions, and the biophysics of animal locomotion.
Contributors: Edlow, Brian L., Mareyam, Azma, Horn, Andreas, Polimeni, Jonathan R., Tisdall, M. Dylan, Augustinack, Jean, Stockmann, Jason P., Diamond, Bram R., Stevens, Allison, Tirrell, Lee S.
... We present an ultra-high resolution magnetic resonance imaging (MRI) dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100 µm isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100 hours of scan time (25 hours per flip angle), allowing derivation of a T1 parameter map and synthesized FLASH volumes. This dataset provides an unprecedented view of the three-dimensional neuroanatomy of the human brain. To optimize the utility of this resource, we warped the dataset into standard stereotactic space. We now distribute the dataset in both native space and stereotactic space to the academic community via multiple platforms. We envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance understanding of human brain anatomy in health and disease.
Contributors: De Petrillo, Francesca, Rosati, Alexandra G.
... Humans can use an intuitive sense of statistics to make predictions about uncertain future events, a cognitive skill that underpins logical and mathematical reasoning. Recent research shows that some of these abilities for statistical inferences can emerge in preverbal infants and non-human primates such as apes and capuchins. An important question is therefore whether animals share the full complement of intuitive reasoning abilities demonstrated by humans, as well as what evolutionary contexts promote the emergence of such skills. Here, we examined whether free-ranging rhesus macaques (Macaca mulatta) can use probability information to infer the most likely outcome of a random lottery, in the first test of whether primates can make such inferences in the absence of direct prior experience. We developed a novel expectancy-violation looking time task, adapted from prior studies of infants, in order to assess the monkeys' expectations. In Study 1, we confirmed that monkeys (n = 20) looked similarly at different sampled items if they had no prior knowledge about the population they were drawn from. In Study 2, monkeys (n = 80) saw a dynamic ‘lottery’ machine containing a mix of two types of fruit outcomes, and then saw either the more common fruit (expected trial) or the relatively rare fruit (unexpected trial) fall from the machine. We found that monkeys looked longer when they witnessed the unexpected outcome. In Study 3, we confirmed that this effect depended on the causal relationship between the sample and the population, not visual mismatch: monkeys (n = 80) looked equally at both outcomes if the experimenter pulled the sampled item from her pocket. These results reveal that rhesus monkeys spontaneously use information about probability to reason about likely outcomes, and show how comparative studies of nonhumans can disentangle the evolutionary history of logical reasoning capacities.
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Contributors: Chen, Hao, Seifikar, Helia, Larocque, Nicholas, Kim, Yvonne, Khatib, Ibrahim, Fernandez, Charles J., Abello, Nicomedes, Robinson, Joshua F.
... While the ramifications associated with polybrominated diphenyl ethers (PBDE) exposures during human pregnancy have yet to be determined, increasing evidence in humans and animal models suggests that these compounds cause neurodevelopmental toxicity. Human embryonic stem cell models (hESCs) can be used to study the effects of environmental chemicals on the successive stages of neuronal development. Here, using a hESC differentiation model, we investigated the effects of common PBDE congeners (BDE-47 or -99) on the successive stages of early neuronal development. First, we determined the points of vulnerability to PBDEs across four stages of in vitro neural development by using assays to assess for cytotoxicity. Differentiated neural progenitors were identified to be more sensitive to PBDEs than their less differentiated counterparts. In follow-up investigations, we observed BDE-47 to inhibit functional processes critical for neurogenesis (e.g., proliferation, migration) in hESC-derived neural precursor cells (NPCs) at sub-lethal concentrations. Finally, to determine the mechanism(s) underlying PBDE-toxicity, we conducted global transcriptomic and methylomic analyses of BDE-47. We identified 589 genes to be differentially expressed (DE) due to BDE-47 exposure, including molecules involved in oxidative stress mediation, cell cycle, hormone signaling, steroid metabolism, and neurodevelopmental pathways. In parallel analyses, we identified a significant increase in CpG methylation. In summary, our results suggest, on a cellular level, PBDEs induce human neurodevelopmental toxicity in a concentration-dependent manner and sensitivity to these compounds is dependent on the developmental stage of exposure. Proposed mRNA and methylomic perturbations may underlie toxicity in early embryonic neuronal populations.
Contributors: Rosati, Alexandra G.
... Objectives: The emergence of human-unique cognitive abilities has been linked to our species' extended juvenile period. Comparisons of cognitive development across species can provide new insights into the evolutionary mechanisms shaping cognition. This study examined the development of different components of spatial memory, cognitive mechanisms that support complex foraging, by comparing two species with similar life history that vary in wild ecology: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). Materials and methods: Spatial memory development was assessed using a cross-sectional experimental design comparing apes ranging from infancy to adulthood. Study 1 tested 73 sanctuary-living apes on a task examining recall of a single location after a 1-week delay, compared to an earlier session. Study 2 tested their ability to recall multiple locations within a complex environment. Study 3 examined a subset of individuals from Study 2 on a motivational control task. Results: In Study 1, younger bonobos and chimpanzees of all ages exhibited improved performance in the test session compared to their initial learning experience. Older bonobos, in contrast, did not exhibit a memory boost in performance after the delay. In Study 2, older chimpanzees exhibited an improved ability to recall multiple locations, whereas bonobos did not exhibit any age-related differences. In Study 3, both species were similarly motivated to search for food in the absence of memory demands. Discussion: These results indicate that closely related species with similar life history characteristics can exhibit divergent patterns of cognitive development, and suggests a role of socioecological niche in shaping patterns of cognition in Pan.
Data from: Are multiple views superior to a single view when teaching hip surgery? a single-blinded randomized controlled trial of technical skill acquisition
Contributors: Wang, Huixiang, Sugand, Kapil, Newman, Simon, Jones, Gareth, Cobb, Justin, Auvinet, Edouard
... Purpose: Surgical education videos currently all use a single point of view (POV) with the trainee locked onto a fixed viewpoint, which may not deliver sufficient information for complex procedures. We developed a novel multiple POV video system and evaluated its training outcome compared with traditional single POV. Methods: We filmed a hip resurfacing procedure performed by an expert attending using 8 cameras in theatre. 30 medical students were randomly and equally allocated to learn the procedure using the multiple POV (experiment group [EG]) versus single POV system (control group [CG]). Participants advanced a pin into the femoral head as demonstrated in the video. We measured the drilling trajectories and compared it with pre-operative plan to evaluate distance of the pin insertion and angular deviations. Two orthopedic attendings expertly evaluated the participants' performance using a modified global rating scale (GRS). There was a pre-video knowledge test that was repeated post-simulation alongside a Likert-scale questionnaire. Results: The angular deviation of the pin in EG was significantly less by 29% compared to CG (p=0.037), with no significant difference in the entry point's distance between groups (p=0.204). The GRS scores for EG were higher than CG (p=0.046). There was a 32% higher overall knowledge test score (p<0.001) and 21% improved Likert-scale questionnaire score (p=0.002) after video-learning in EG than CG, albeit no significant difference in the knowledge test score before video-learning (p=0.721). Conclusion: The novel multiple POV provided significant objective and subjective advantages over single POV for acquisition of technical skills in hip surgery.
Contributors: Wang, Shaohe, Ochoa, Stacy D., Khaliullin, Renat N., Gerson-Gurwitz, Adina, Hendel, Jeffrey M., Zhao, Zhiling, Biggs, Ronald, Chisholm, Andrew D., Desai, Arshad, Oegema, Karen
... The C. elegans embryo is an important model for analyzing mechanisms of cell fate specification and tissue morphogenesis. Sophisticated lineaging approaches for analyzing embryogenesis have been developed but are labor-intensive and do not naturally integrate morphogenetic readouts. To enable the rapid classification of developmental phenotypes, we developed a high-content method that employs two custom strains: a Germ Layer strain expressing nuclear markers in the ectoderm, mesoderm and endoderm/pharynx, and a Morphogenesis strain expressing markers labeling epidermal cell junctions and the neuronal cell surface. We describe a procedure that allows simultaneous live imaging of development in 80-100 embryos and provide a custom program that generates cropped, oriented image stacks of individual embryos to facilitate analysis. We demonstrate the utility of our method by perturbing 40 previously characterized developmental genes in variants of the two strains containing RNAi-sensitizing mutations. The resulting datasets yielded distinct, reproducible signature phenotypes for a broad spectrum of genes involved in cell fate specification and morphogenesis. Our analysis additionally provides new in vivo evidence for MBK-2 function in mesoderm fate specification and LET-381 function in elongation.
Data from: Lethal and sublethal synergistic effects of a new systemic pesticide, flupyradifurone (Sivanto®) on honey bees
Contributors: Tosi, Simone, Nieh, James
... The honey bee (Apis mellifera L.) is an important pollinator and a model for pesticide effects on insect pollinators. The effects of agricultural pesticides on honey bee health have therefore raised concern. Bees can be exposed to multiple pesticides that may interact synergistically, amplifying their side-effects. Attention has focused on neonicotinoid pesticides, but flupyradifurone (FPF) is a novel butenolide insecticide that is also systemic and a nicotinic acetylcholine receptor (nAChR) agonist. We therefore tested the lethal and sublethal toxic effects of FPF over different seasons and worker types, and the interaction of FPF with a common SBI fungicide, propiconazole. We provide the first demonstration of adverse synergistic effects on bee survival and behaviour (poor coordination, hyperactivity, apathy) at field-realistic doses. Pesticide effects were significantly influenced by worker type and season. Foragers were consistently more susceptible to these pesticides (4-fold greater effect) than in-hive bees, and both worker types were more strongly affected by FPF in summer as compared to spring. Because risk assessment requires relatively limited tests that only marginally address bee behaviour and do not consider the influence of bee age and season, our results raise concerns about the safety of approved pesticides, including FPF. We suggest that pesticide risk assessment also test for common chemical mixture synergies on behaviour and survival.
Contributors: Garwood, Russell J., Spencer, Alan R. T., Sutton, Mark D.
... Macroevolutionary processes dictate the generation and loss of biodiversity. Understanding them is a key challenge when interrogating the earth-life system in deep time. Model-based approaches can reveal important macroevolutionary patterns, and generate hypotheses on the underlying processes. Here we present and document a novel model called REvoSim (Rapid Evolutionary Simulator) coupled with a software implementation of this model. The latter is available here as both source code (C++/Qt, GNU General Public License), and as distributables for a variety of operating systems. REvoSim is an individual-based model with a strong focus on computational efficiency. It can simulate populations of 105–107 digital organisms over geological timescales on a typical desktop computer, and incorporates spatial and temporal environmental variation, recombinant reproduction, mutation and dispersal. Whilst microevolutionary processes drive the model, macroevolutionary phenomena such as speciation and extinction emerge. We present results and analysis of the model focussing on validation, and note a number potential applications. REvoSim can serve as a multipurpose platform for studying both macro- and microevolution, and bridges this divide. It will be continually developed by the authors to expand its capabilities and hence its utility.
Contributors: Eliason, Chad, Andersen, Michael, Hackett, Shannon
... Color is among the most striking features of organisms, varying not only in spectral properties like hue and brightness, but also in where and how it is produced on the body. Different combinations of colors on a bird’s body are important in both environmental and social contexts. Previous comparative studies have treated plumage patches individually or derived plumage complexity scores from color measurements across a bird’s body. However, these approaches do not consider the multivariate nature of plumages (allowing for plumage to evolve as a whole) or account for interpatch distances. Here, we leverage a rich toolkit used in historical biogeography to assess color pattern evolution in a cosmopolitan radiation of birds, kingfishers (Aves: Alcedinidae). We demonstrate the utility of this approach and test hypotheses about the tempo and mode of color evolution in kingfishers. Our results highlight the importance of considering interpatch distances in understanding macroevolutionary trends in color diversity and demonstrate how historical biogeography models are a useful way to model plumage color pattern evolution. Furthermore, they show that distinct color mechanisms (pigments or structural colors) spread across the body in different ways and at different rates. Specifically, net rates are higher for structural colors than pigment-based colors. Together, our study suggests a role for both development and selection in driving extraordinary color pattern diversity in kingfishers. We anticipate this approach will be useful for modeling other complex phenotypes besides color, such as parasite evolution across the body.