Journal of the Royal Society. Interface

Journal: Journal of the Royal Society. Interface

Abbreviation

J. R. Soc. Interface

Publisher

Royal Society

ISSN

1742-5689
1742-5662

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Publications 1 - 10 of 105

Unmasking structural patterns in incidence matrices: an application to ecological data
Bramon Mora, Bernat; Dalla Riva, Giulio V.; Stouffer, Daniel B. (2019)
Journal of the Royal Society. Interface
Null models have become a crucial tool for understanding structure within incidence matrices across multiple biological contexts. For example, they have been widely used for the study of ecological and biogeographic questions, testing hypotheses regarding patterns of community assembly, species co-occurrence and biodiversity. However, to our knowledge we remain without a general and flexible approach to study the mechanisms explaining such structures. Here, we provide a method for generating ‘correlation-informed’ null models, which combine the classic concept of null models and tools from community ecology, like joint statistical modelling. Generally, this model allows us to assess whether the information encoded within any given correlation matrix is predictive for explaining structural patterns observed within an incidence matrix. To demonstrate its utility, we apply our approach to two different case studies that represent examples of common scenarios encountered in community ecology. First, we use a phylogenetically informed null model to detect a strong evolutionary fingerprint within empirically observed food webs, reflecting key differences in the impact of shared evolutionary history when shaping the interactions of predators or prey. Second, we use multiple informed null models to identify which factors determine structural patterns of species assemblages, focusing in on the study of nestedness and the influence of site size, isolation, species range and species richness. In addition to offering a versatile way to study the mechanisms shaping the structure of any incidence matrix, including those describing ecological communities, our approach can also be adapted further to test even more sophisticated hypotheses.
Brilliant cresyl blue enhanced optoacoustic imaging enables non-destructive imaging of mammalian ovarian follicles for artificial reproduction: Brilliant cresyl blue enhanced optoacoustic imaging enables non-destructive imaging of mammalian ovarian follicles for artificial reproduction
Dutta, Rahul; Mandal, Subhamoy; Lin, Hsiao-Chun A.; et al. (2020)
Journal of the Royal Society. Interface
In the field of reproductive biology, there is a strong need for a suitable tool capable of non-destructive evaluation of oocyte viability and function. We studied the application of brilliant cresyl blue (BCB) as an intra-vital exogenous contrast agent using multispectral optoacoustic tomography (MSOT) for visualization of porcine ovarian follicles. The technique provided excellent molecular sensitivity, enabling the selection of competent oocytes without disrupting the follicles. We further conducted in vitro embryo culture, molecular analysis (real-time and reverse transcriptase polymerase chain reaction) and DNA fragmentation analysis to comprehensively establish the safety of BCB-enhanced MSOT imaging in monitoring oocyte viability. Overall, the experimental results suggest that the method offers a significant advance in the use of contrast agents and molecular imaging for reproductive studies. Our technique improves the accurate prediction of ovarian reserve significantly and, once standardized for in vivo imaging, could provide an effective tool for clinical infertility management.
Dynamic disorder in simple enzymatic reactions induces stochastic amplification of substrate
Gupta, Ankit; Milias-Argeitis, Andreas; Khammash, Mustafa Hani (2017)
Journal of the Royal Society. Interface
The digital traces of bubbles
Garcia, David; Tessone, Claudio J.; Mavrodiev, Pavlin; et al. (2014)
Journal of the Royal Society. Interface
Quantifying long-term evolution of intra-urban spatial interactions
Sun, Lijun; Jin, Jian Gang; Axhausen, Kay W.; et al. (2015)
Journal of the Royal Society. Interface
Optical coherence elastography by ambient pressure modulation for high-resolution strain mapping applied to patterned cross-linking
Kling, Sabine (2020)
Journal of the Royal Society. Interface
Techniques to assess bone ultrastructure organization: orientation and arrangement of mineralized collagen fibrils
Georgiadis, Marios; Müller, Ralph; Schneider, Philipp (2016)
Journal of the Royal Society. Interface
Mechanical regulation of bone formation and resorption around implants in a mouse model of osteopenic bone
Li, Zihui; Betts, Duncan; Kuhn, Gisela; et al. (2019)
Journal of the Royal Society. Interface
Hydrodynamics of the leucon sponge pump
Asadzadeh, Seyed S.; Larsen, Poul S.; Riisgard, Hans U.; et al. (2019)
Journal of the Royal Society. Interface
Gradual conversion of cellular stress patterns into pre-stressed matrix architecture during in vitro tissue growth
Bidan, Cécile M.; Kollmannsberger, Philip; Gering, Vanessa; et al. (2016)
Journal of the Royal Society. Interface

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