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  1. Article: Wavelet testing for a replicate-effect within an ordered multiple-trial experiment

    Embleton, Jonathan / Knight, Marina I. / Ombao, Hernando

    Elsevier B.V. Computational statistics & data analysis. 2022 Feb. 15,

    2022  

    Abstract: Experimental time series data collected across a sequence of ordered trials (replicates) often crop up in many fields, from neuroscience to circadian biology. In order to decide when to appropriately evade the simplifying assumption that all replicates ... ...

    Abstract Experimental time series data collected across a sequence of ordered trials (replicates) often crop up in many fields, from neuroscience to circadian biology. In order to decide when to appropriately evade the simplifying assumption that all replicates stem from the same process, an assumption often untrue even when identical stimuli are applied, two novel tests are proposed that assess whether a significant trial-effect is manifest along the experiment. The modelling framework uses wavelet multiscale constructions that mitigate against the potential nonstationarities often present in experimental data, both across times and across replicates. The proposed tests are evaluated in thorough simulation studies and illustrated on neuroscience data, proving to be flexible tools with great promise in dealing with complex multiple-trials time series data and allowing the analyst to accordingly tune their subsequent analysis.
    Keywords neurophysiology ; statistics ; time series analysis ; wavelet
    Language English
    Dates of publication 2022-0215
    Publishing place Elsevier B.V.
    Document type Article
    Note Pre-press version
    ZDB-ID 1478763-5
    ISSN 0167-9473
    ISSN 0167-9473
    DOI 10.1016/j.csda.2022.107456
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Multiple metals influence distinct properties of the Arabidopsis circadian clock.

    Hargreaves, Jessica K / Oakenfull, Rachael J / Davis, Amanda M / Pullen, Freya / Knight, Marina I / Pitchford, Jon W / Davis, Seth J

    PloS one

    2022  Volume 17, Issue 4, Page(s) e0258374

    Abstract: Circadian rhythms coordinate endogenous events with external signals, and are essential to biological function. When environmental contaminants affect these rhythms, the organism may experience fitness consequences such as reduced growth or increased ... ...

    Abstract Circadian rhythms coordinate endogenous events with external signals, and are essential to biological function. When environmental contaminants affect these rhythms, the organism may experience fitness consequences such as reduced growth or increased susceptibility to pathogens. In their natural environment plants may be exposed to a wide range of industrial and agricultural soil pollutants. Here, we investigate how the addition of various metal salts to the root-interaction environment can impact rhythms, measured via the promoter:luciferase system. The consequences of these environmental changes were found to be varied and complex. Therefore, in addition to traditional Fourier-based analyses, we additionally apply novel wavelet-based spectral hypothesis testing and clustering methodologies to organize and understand the data. We are able to classify broad sets of responses to these metal salts, including those that increase, and those that decrease, the period, or which induce a lack of precision or disrupt any meaningful periodicity. Our methods are general, and may be applied to discover common responses and hidden structures within a wide range of biological time series data.
    MeSH term(s) Arabidopsis/physiology ; Arabidopsis Proteins/genetics ; Circadian Clocks ; Circadian Rhythm/physiology ; Salts
    Chemical Substances Arabidopsis Proteins ; Salts
    Language English
    Publishing date 2022-04-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0258374
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: A wavelet lifting approach to long-memory estimation.

    Knight, Marina I / Nason, Guy P / Nunes, Matthew A

    Statistics and computing

    2016  Volume 27, Issue 6, Page(s) 1453–1471

    Abstract: Reliable estimation of long-range dependence parameters is vital in time series. For example, in environmental and climate science such estimation is often key to understanding climate dynamics, variability and often prediction. The challenge of data ... ...

    Abstract Reliable estimation of long-range dependence parameters is vital in time series. For example, in environmental and climate science such estimation is often key to understanding climate dynamics, variability and often prediction. The challenge of data collection in such disciplines means that, in practice, the sampling pattern is either irregular or blighted by missing observations. Unfortunately, virtually all existing Hurst parameter estimation methods assume regularly sampled time series and require modification to cope with irregularity or missing data. However, such interventions come at the price of inducing higher estimator bias and variation, often worryingly ignored. This article proposes a new Hurst exponent estimation method which naturally copes with data sampling irregularity. The new method is based on a multiscale lifting transform exploiting its ability to produce wavelet-like coefficients on irregular data and, simultaneously, to effect a necessary powerful decorrelation of those coefficients. Simulations show that our method is accurate and effective, performing well against competitors even in regular data settings. Armed with this evidence our method sheds new light on long-memory intensity results in environmental and climate science applications, sometimes suggesting that different scientific conclusions may need to be drawn.
    Language English
    Publishing date 2016-09-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2017741-0
    ISSN 1573-1375 ; 0960-3174
    ISSN (online) 1573-1375
    ISSN 0960-3174
    DOI 10.1007/s11222-016-9698-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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  4. Article: Timely Questions Emerging in Chronobiology: The Circadian Clock Keeps on Ticking.

    Chawla, Sangeeta / O'Neill, John / Knight, Marina I / He, Yuqing / Wang, Lei / Maronde, Erik / Rodríguez, Sergio Gil / van Ooijen, Gerben / Garbarino-Pico, Eduardo / Wolf, Eva / Dkhissi-Benyahya, Ouria / Nikhat, Anjoom / Chakrabarti, Shaon / Youngstedt, Shawn D / Zi-Ching Mak, Natalie / Provencio, Ignacio / Oster, Henrik / Goel, Namni / Caba, Mario /
    Oosthuizen, Maria / Duffield, Giles E / Chabot, Christopher / Davis, Seth J

    Journal of circadian rhythms

    2024  Volume 22, Page(s) 2

    Abstract: Chronobiology investigations have revealed much about cellular and physiological clockworks but we are far from having a complete mechanistic understanding of the physiological and ecological implications. Here we present some unresolved questions in ... ...

    Abstract Chronobiology investigations have revealed much about cellular and physiological clockworks but we are far from having a complete mechanistic understanding of the physiological and ecological implications. Here we present some unresolved questions in circadian biology research as posed by the editorial staff and guest contributors to the Journal of Circadian Rhythms. This collection of ideas is not meant to be comprehensive but does reveal the breadth of our observations on emerging trends in chronobiology and circadian biology. It is amazing what could be achieved with various expected innovations in technologies, techniques, and mathematical tools that are being developed. We fully expect strengthening mechanistic work will be linked to health care and environmental understandings of circadian function. Now that most clock genes are known, linking these to physiological, metabolic, and developmental traits requires investigations from the single molecule to the terrestrial ecological scales. Real answers are expected for these questions over the next decade. Where are the circadian clocks at a cellular level? How are clocks coupled cellularly to generate organism level outcomes? How do communities of circadian organisms rhythmically interact with each other? In what way does the natural genetic variation in populations sculpt community behaviors? How will methods development for circadian research be used in disparate academic and commercial endeavors? These and other questions make it a very exciting time to be working as a chronobiologist.
    Language English
    Publishing date 2024-04-02
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2126348-6
    ISSN 1740-3391
    ISSN 1740-3391
    DOI 10.5334/jcr.237
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: EgoActive: Integrated Wireless Wearable Sensors for Capturing Infant Egocentric Auditory-Visual Statistics and Autonomic Nervous System Function 'in the Wild'.

    Geangu, Elena / Smith, William A P / Mason, Harry T / Martinez-Cedillo, Astrid Priscilla / Hunter, David / Knight, Marina I / Liang, Haipeng / Del Carmen Garcia de Soria Bazan, Maria / Tse, Zion Tsz Ho / Rowland, Thomas / Corpuz, Dom / Hunter, Josh / Singh, Nishant / Vuong, Quoc C / Abdelgayed, Mona Ragab Sayed / Mullineaux, David R / Smith, Stephen / Muller, Bruce R

    Sensors (Basel, Switzerland)

    2023  Volume 23, Issue 18

    Abstract: There have been sustained efforts toward using naturalistic methods in developmental science to measure infant behaviors in the real world from an egocentric perspective because statistical regularities in the environment can shape and be shaped by the ... ...

    Abstract There have been sustained efforts toward using naturalistic methods in developmental science to measure infant behaviors in the real world from an egocentric perspective because statistical regularities in the environment can shape and be shaped by the developing infant. However, there is no user-friendly and unobtrusive technology to densely and reliably sample life in the wild. To address this gap, we present the design, implementation and validation of the EgoActive platform, which addresses limitations of existing wearable technologies for developmental research. EgoActive records the active infants' egocentric perspective of the world via a miniature wireless head-mounted camera concurrently with their physiological responses to this input via a lightweight, wireless ECG/acceleration sensor. We also provide software tools to facilitate data analyses. Our validation studies showed that the cameras and body sensors performed well. Families also reported that the platform was comfortable, easy to use and operate, and did not interfere with daily activities. The synchronized multimodal data from the EgoActive platform can help tease apart complex processes that are important for child development to further our understanding of areas ranging from executive function to emotion processing and social learning.
    MeSH term(s) Infant ; Child ; Humans ; Wearable Electronic Devices ; Software ; Technology ; Autonomic Nervous System
    Language English
    Publishing date 2023-09-16
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s23187930
    Database MEDical Literature Analysis and Retrieval System OnLINE

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