Contractile deficits in engineered cardiac microtissues as a result of MYBPC3 deficiency and mechanical overload.

The integration of in vitro cardiac tissue models, human induced pluripotent stem cells (hiPSCs) and genome-editing tools allows for the enhanced interrogation of physiological phenotypes and recapitulation of disease pathologies. Here, using a cardiac tissue model consisting of filamentous three-dimensional matrices populated with cardiomyocytes derived from healthy wild-type (WT) hiPSCs (WT hiPSC-CMs) or isogenic hiPSCs deficient in the sarcomere protein cardiac myosin-binding protein C (MYBPC3-/- hiPSC-CMs), we show that the WT microtissues adapted to the mechanical environment with increased contraction force commensurate to matrix stiffness, whereas the MYBPC3-/- microtissues exhibited impaired force development kinetics regardless of matrix stiffness and deficient contraction force only when grown on matrices with high fibre stiffness. Under mechanical overload, the MYBPC3-/- microtissues had a higher degree of calcium transient abnormalities, and exhibited an accelerated decay of calcium dynamics as well as calcium desensitization, which accelerated when contracting against stiffer fibres. Our findings suggest that MYBPC3 deficiency and the presence of environmental stresses synergistically lead to contractile deficits in cardiac tissues

Beak shape and nest material use in birds

This work was supported by a BBSRC Discovery Fellowship (grant no. BB/S01019X/1); the John Templeton Foundation (grant no. 60501); and the European Research Council (grant no. 788203).The evolution of behaviour can both influence, and be influenced by, morphology. Recent advances in methods and data availability have facilitated broad-scale investigations of physical form and behavioural function in many contexts, but the relationship between animal morphology and object manipulation-particularly objects used in construction-remains largely unknown. Here, we employ a new global database of nest materials used by 5924 species of birds together with phylogenetically informed random forest models to evaluate the link between beak shape and these nest-building materials. We find that beak morphology, together with species diet and access to materials, can predict nest-material use above chance and with high accuracy (68-97%). Much of this relationship, however, is driven by phylogenetic signal and sampling biases. We therefore conclude that while variation in nest material use is linked with that of beak shape across bird species, these correlations are modulated by the ecological context and evolutionary history of these species.Publisher PDFPeer reviewe

Web-Based Simulation: Evolution or Revolution?

ACM Transactions on Modeling and Computer Simulation, Vol. 10, No. 1, January 2000, Pages 3–17

A Multi-Epoch HST Study of the Herbig-Haro Flow from XZ Tauri

We present nine epochs of Hubble Space Telescope optical imaging of the bipolar outflow from the pre-main sequence binary XZ Tauri. Our data monitors the system from 1995-2005 and includes emission line images of the flow. The northern lobe appears to be a succession of bubbles, the outermost of which expanded ballistically from 1995-1999 but in 2000 began to deform and decelerate along its forward edge. It reached an extent of 6" from the binary in 2005. A larger and fainter southern counterbubble was detected for the first time in deep ACS images from 2004. Traces of shocked emission are seen as far as 20" south of the binary. The bubble emission nebulosity has a low excitation overall, as traced by the [S II]/H-alpha line ratio, requiring a nearly comoving surrounding medium that has been accelerated by previous ejections or stellar winds. Within the broad bubbles there are compact emission knots whose alignments and proper motions indicate that collimated jets are ejected from each binary component. The jet from the southern component, XZ Tau A, is aligned with the outflow axis of the bubbles and has tangential knot velocities of 70-200 km/s. Knots in the northern flow are seen to slow and brighten as they approach the forward edge of the outermost bubble. The knots in the jet from the other star, XZ Tau B, have lower velocities of ~100 km/s

Dublin's participation in the predicting media memorability task at MediaEval 2018

This paper outlines 6 approaches taken to computing video memorability, for the MediaEval media memorability task. The approaches are based on video features, an end-to-end approach, saliency, aesthetics, neural feedback, and an ensemble of all approaches

Exploring EEG for object detection and retrieval

This paper explores the potential for using Brain Computer Interfaces (BCI) as a relevance feedback mechanism in contentbased image retrieval. Several experiments are performed using a rapid serial visual presentation (RSVP) of images at different rates (5Hz and 10Hz) on 8 users with different degrees of familiarization with BCI and the dataset. We compare the feedback from the BCI and mouse-based interfaces in a subset of TRECVid images, finding that, when users have limited time to annotate the images, both interfaces are comparable in performance. Comparing our best users in a retrieval task, we found that EEG-based relevance feedback can outperform mouse-based feedback

Temporal Gene Expression Profiling during Rat Femoral Marrow Ablation-Induced Intramembranous Bone Regeneration

Enhanced understanding of differential gene expression and biological pathways associated with distinct phases of intramembranous bone regeneration following femoral marrow ablation surgery will improve future advancements regarding osseointegration of joint replacement implants, biomaterials design, and bone tissue engineering. A rat femoral marrow ablation model was performed and genome-wide microarray data were obtained from samples at 1, 3, 5, 7, 10, 14, 28, and 56 days post-ablation, with intact bones serving as controls at Day 0. Bayesian model-based clustering produced eight distinct groups amongst 9,062 significant gene probe sets based on similar temporal expression profiles, which were further categorized into three major temporal classes of increased, variable, and decreased expression. Osteoblastic- and osteoclastic-associated genes were found to be significantly expressed within the increased expression groups. Chondrogenesis was not detected histologically. Adipogenic marker genes were found within variable/decreased expression groups, emphasizing that adipogenesis was inhibited during osteogenesis. Differential biological processes and pathways associated with each major temporal group were identified, and significantly expressed genes involved were visually represented by heat maps. It was determined that the increased expression group exclusively contains genes involved in pathways for matrix metalloproteinases (MMPs), Wnt signaling, TGF-β signaling, and inflammatory pathways. Only the variable expression group contains genes associated with glycolysis and gluconeogenesis, the notch signaling pathway, natural killer cell mediated cytotoxicity, and the B cell receptor signaling pathway. The decreased group exclusively consists of genes involved in heme biosynthesis, the p53 signaling pathway, and the hematopoietic cell lineage. Significant biological pathways and transcription factors expressed at each time point post-ablation were also identified. These data present the first temporal gene expression profiling analysis of the rat genome during intramembranous bone regeneration induced by femoral marrow ablation

Nest traits for the world's birds

Funding: H2020 European Research Council, Grant/Award Number: 788203; John Templeton Foundation, Grant/Award Number: 60501.Motivation: A well-constructed nest is a key element of successful reproduction in most species of birds, and nest morphology varies widely across the class. Macroecological and macroevolutionary studies tend to group nest design into a small number of discrete categories, often based on taxonomic inference. In reality, however, many species display considerable intraspecific variation in their nest-building behaviour, and broad-level categories may include several functionally distinct nest types. To address this imprecision in the literature and facilitate future studies of broad-scale variation in avian parental care, we here introduce a detailed, global comparative database of nest building in birds, together with preliminary correlations between these traits and species-level environmental variables. Main types of variables contained: We present species-level data for nest structure, location, height, material composition, sex of builder, building time and nest dimensions. Spatial location and grain: Global. Maps are presented at the 10 × 10 level. Time period and grain: Included species are generally extant, although we present some data for recently extinct taxa. The data were collected in 2017–2021 and was drawn from secondary sources published in 1992–2021. Major taxa and level of measurement: Partial or complete trait data is presented for 8601 species of birds, representing 36 of 36 orders and 239 of 243 families. Software format: Data have been uploaded as Supplementary Material in .csv format and are separated by species and source for all traits (Dataset S1, and Metadata) as well as summarized at the species level for the major structure and location variables (Dataset S2, and Metadata).Publisher PDFPeer reviewe

How interaction methods affect image segmentation: User experience in the task

Interactive image segmentation is extensively used in photo editing when the aim is to separate a foreground object from its background so that it is available for various applications. The goal of the interaction is to get an accurate segmentation of the object with the minimal amount of human effort. To improve the usability and user experience using interactive image segmentation we present three interaction methods and study the effect of each using both objective and subjective metrics, such as, accuracy, amount of effort needed, cognitive load and preference of interaction method as voted by users. The novelty of this paper is twofold. First , the evaluation of interaction methods is carried out with objective metrics such as object and boundary accuracies in tandem with subjective metrics to cross check if they support each other. Second, we analyze Electroencephalography (EEG) data obtained from subjects perform- ing the segmentation as an indicator of brain activity. The experimental results potentially give valuable cues for the development of easy-to-use yet efficient interaction methods for image segmentation