Reinterpreting turbidity: new methodologies for suspended-sediment research

Existing instruments for turbidity measurement vary considerably in terms of the principles of operation, the physical design, and the cost to the researcher. The operational methodologies of late twentieth century turbidity instruments have led to the development of new turbidity measurement standards, and the invention of new turbidity measurement units. These measurement units are invalid and do not have a sound footing with regard to the underlying physics of the scattering and absorption of light by suspended particles. A review of the turbidity literature has shown that the proliferation of these incommensurate units of measurement throughout the physical sciences has caused extensive misinterpretation of turbidity data, particularly concerning its use as a surrogate for suspended sediment concentration (SSC). Turbidity is a complex phenomenon, and its measurement reported in terms of a single numeric quantity in some physically indeterminate units of measurement. It is not necessarily useful to reduce complex data to a single value, since this approach does not permit the researcher any a posteriori opportunity to reinterpret existing data in light of innovations in analysis methodology. This thesis proposes a new way to present turbidity data that will facilitate the cross-comparison of turbidity measurements made by different instruments on any type of suspended sediment. The creation of a new turbidity research instrument that illustrates the application of the new method for reporting turbidity data as a ratio of light attenuation values in decibels, promotes a positive change in direction away from the traditional measurement units. The design process focusses on the instrument calibration procedure. With a simple reinterpretation of the phase-function description of light scattering from suspended particles, measurements of light attenuation made at multiple angles with respect to the axis of the incident light beam, compare easily with the same measurements made using different wavelengths of incident light. This work goes on to introduce new nomenclature that requires the citing of measurement angle and wavelength of light to be an integral part of any recorded turbidity measurement. A modelling approach is used in the evaluation of the new turbidity instrument. This modelling is important for three reasons. First, it identifies which instrument parameters affect the result of a turbidity measurement – the key parameter being the mathematical function that describes the spatial divergence of the incident light beam, which is important to measurement systems that employ incoherent light sources such as LEDs, rather than to laser-based systems. Secondly, the modelling reveals two fundamental theories of light scattering due to suspended particles, both of which are required to describe adequately the turbidity of sediment-laden water. These two theories are Mie scattering and geometric optics. Mie scattering is well accounted for by the developed model - geometric optics, less so. The extent to which the model predictions diverge from the empirical data is characterised by a metric related to the backscatter fraction, and the consistency and linearity of the model is established. Ideas for the improvement of the geometric optics feature of the model are discussed, as is the third reason for the importance of numerical modelling. This third reason relates to the use of multi-parameter turbidity measurements as a means to characterise the properties of a suspended sediment. By simulating precisely the measurement response of the turbidity instrument, then it is notionally possible to infer the properties of an unknown sediment by tuning the model parameters to match the empirical response of the unknown sediment. This tuning process could reveal information pertaining to particle size and shape. Finally, potential applications for the new research instrument focus on improvements to the instrument itself and the methodology, and the further development of the turbidity data reporting nomenclature. Prototype methodologies that relate turbidity to suspended sediment concentration are suggested, which also consider ways in which the optical measurements can potentially classify the physical properties of a sediment

Experimental investigation into the impact of a liquid droplet onto a granular bed using three-dimensional, time-resolved, particle tracking

This article was published in the journal, Physical Review E [ © American Physical Society] and the definitive version is available at: http://dx.doi.org/10.1103/PhysRevE.89.032201An experimental investigation into the interaction that occurs between an impacting water droplet and a granular bed of loose graded sand has been carried out. High-speed imaging, three-dimensional time-resolved particle tracking, and photogrammetric surface profiling have been used to examine individual impact events. The focus of the study is the quantification and trajectory analysis of the particles ejected from the sand bed, along with measurement of the change in bed morphology. The results from the experiments have detailed two distinct mechanisms of particle ejection: the ejection of water-encapsulated particles from the edge of the wetted region and the ejection of dry sand from the periphery of the impact crater. That the process occurs by these two distinct mechanisms has hitherto been unobserved. Presented in the paper are distributions of the particle ejection velocities, angles, and transport distances for both mechanisms. The ejected water-encapsulated particles, which are few in number, are characterized by low ejection angles and high ejection velocities, leading to large transport distances; the ejected dry particles, which are much greater in number, are characterized by high ejection angles and low velocities, leading to lower transport distances. From the particle ejection data, the momentum of the individual ballistic sand particles has been calculated; it was found that only 2% of the water-droplet momentum at impact is transferred to the ballistic sand particles. In addition to the particle tracking, surface profiling of the granular bed postimpact has provided detailed information on its morphology; these data have demonstrated the consistent nature of the craters produced by the impact and suggest that particle agglomerations released from their edges make up about twice the number of particles involved in ballistic ejection. It is estimated that, overall, about 4% of the water-droplet momentum is taken up in particle movement

The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer.

Aberrant DNA methylation is an important cancer hallmark, yet the dynamics of DNA methylation changes in human carcinogenesis remain largely unexplored. Moreover, the role of DNA methylation for prediction of clinical outcome is still uncertain and confined to specific cancers. Here we perform the most comprehensive study of DNA methylation changes throughout human carcinogenesis, analysing 27,578 CpGs in each of 1,475 samples, ranging from normal cells in advance of non-invasive neoplastic transformation to non-invasive and invasive cancers and metastatic tissue. We demonstrate that hypermethylation at stem cell PolyComb Group Target genes (PCGTs) occurs in cytologically normal cells three years in advance of the first morphological neoplastic changes, while hypomethylation occurs preferentially at CpGs which are heavily Methylated in Embryonic Stem Cells (MESCs) and increases significantly with cancer invasion in both the epithelial and stromal tumour compartments. In contrast to PCGT hypermethylation, MESC hypomethylation progresses significantly from primary to metastatic cancer and defines a poor prognostic signature in four different gynaecological cancers. Finally, we associate expression of TET enzymes, which are involved in active DNA demethylation, to MESC hypomethylation in cancer. These findings have major implications for cancer and embryonic stem cell biology and establish the importance of systemic DNA hypomethylation for predicting prognosis in a wide range of different cancers

Data from: Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric data sets derived from Sulawesi’s three largest mammals: the Babirusa, Anoa, and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Myr ago to 2-3 Myr ago), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (~1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years

Reflective Personality: Identifying Cognitive Style and Cognitive Complexity

Categorized among learning practices, reflection involves cognitive processing. Some people say they reflect often, whereas others claim they are less inclined to reflect on a regular basis. The present study examines reflection in an academic learning setting. In contrast with previous studies testing reflective task accomplishment, we are interested in personality traits that can predict reflection or a reflective outcome. By means of a survey university students are questioned about their learning practices when working on their final thesis. To test whether certain traits influence reflection and whether reflection produces cognitive outcomes at the individual level, we performed hierarchical regression analysis. In addition, structural equation modeling is used to test for the mediation effects of reflection. The data stress a mediating role of reflection in the relationship between particular personality traits and cognitive complexity

Materials and Methods, Supplementary Tables and Supplementary Figures from Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the Babirusa, Anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2–3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years

Palaeontology from Australasia and beyond: Abstracts from Palaeo Down Under 3 Perth, Western Australia, July 2023

Palaeo Down Under 3 (PDU3), the now quadrennial conference of the Australasian Palaeontologists (AAP) association, was held in Perth, Western Australia, from the 10th-14th of July 2023. PDU3 showcased innovative research, outreach and education initiatives being conducted across Australasia and beyond by both local and international scientists. A total of 78 talks, 17 posters and 6 plenaries were presented across the five days, and covered a wide range of topics, geological timeframes, and fossil groups. AAP is proud to publish this compilation of PDU3 abstracts to illustrate the current and ongoing strength of Australasian palaeontology. Sarah K. Martin [ [email protected] ], Geological Survey of Western Australia, Department of Energy, Mines, Industry Regulation and Safety, 100 Plain St, East Perth, Western Australia 6004, Australia; Michael Archer [ [email protected] ], School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia; Heidi J. Allen [ [email protected] ], Geological Survey of Western Australia, Department of Energy, Mines, Industry Regulation and Safety, 100 Plain St, East Perth, Western Australia 6004, Australia; Daniel D. Badea [ [email protected] ], Faculty of Geography and Geology, "Alexandru Ioan Cuza" University, Bulevard "Carol I", Nr.11, 707006, Iași, Romania; Eleanor Beidatsch [ [email protected] ], Palaeoscience Research Centre, University of New England, Armidale, New South Wales 2351, Australia; Marissa J. Betts [ [email protected] ], Palaeoscience Research Centre/LLUNE, University of New England, Armidale, New South Wales 2351, Australia; Maria Blake [ [email protected] ], School of Earth, Atmosphere and Environment, Monash University, 9 Rainforest Walk, Clayton, Victoria 3800, Australia; Phillip C. Boan [ [email protected] ], University of California, Riverside, Geology 1242, 900 University Ave, Riverside, CA 92521, U.S.A.; Tory Botha [ [email protected] ], School of Biological Sciences, Molecular Life Sciences Building, North Terrace Campus, The University of Adelaide, Adelaide, South Australia 5005, Australia; Glenn A. Brock [ [email protected] ], School of Natural Sciences, Macquarie University, New South Wales 2109, Australia; Luke Brosnan [ [email protected] ], WA Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Building 500, Curtin University, Kent St, Bentley, Western Australia 6102, Australia; Jack Castle-Jones [ [email protected] ], School of Natural Sciences, Macquarie University, New South Wales 2109, Australia; Jonathan Cramb [ [email protected] ], Queensland Museum, PO Box 3300, South Brisbane BC, Queensland 4101, Australia; Vanesa L. De Pietri [ [email protected] ], School of Earth and Environment, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Sherri Donaldson [ [email protected] ], School of Geosciences, University of Edinburgh, Grant Institute, The King's Buildings, James Hutton Road, Edinburgh, EH9 3FE, Scotland, U.K.; Elizabeth M. Dowding [ [email protected] ], Friedrich-Alexander-Universität Erlangen-Nürnberg, Loewenichstraße 28 91054 Erlangen, Germany; Ruairidh Duncan [ [email protected] ], Evans EvoMorph Lab, Room 226, 18 Innovation Walk, School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia; Amy L. Elson [ [email protected] ], WA Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Building 500, Curtin University, Kent St, Bentley, Western Australia 6102, Australia; Roy M. Farman [ [email protected] ], School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia; Mahala A. Fergusen [ [email protected] ], School of Biological Sciences, Benham Building, North Terrace Campus, The University of Adelaide, Adelaide, South Australia 5005, Australia; Alyssa Fjeld [ [email protected] ], School of Biological Sciences, 18 Innovation Walk, Monash University, Clayton, Victoria 3800, and School of Natural Sciences, Macquarie University, New South Wales 2109, Australia; David Flannery [ [email protected] ], School of Earth and Atmospheric Sciences, Queensland University of Technology, 2 George St, Brisbane, Queensland 4000, Australia; Timothy G. Frauenfelder [ [email protected] ], University of New England, Armidale, New South Wales 2351, Australia; John D. Gorter [ [email protected] ], PO Box 711, Claremont, Western Australia 6910, Australia; Michelle Gray [ [email protected] ], School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3216, Australia; Nigel Gray [ [email protected] ], GPO Box 2902, Brisbane, Queensland 4001, Australia; Peter Haines [ [email protected] ], Geological Survey of Western Australia, Department of Energy, Mines, Industry Regulation and Safety, 100 Plain St, East Perth, Western Australia 6004, Australia; Lachlan J. Hart [ [email protected] ], Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia; Brooke E. Holland [ [email protected] ], School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia; James D. Holmes [ [email protected] ], Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden; Lars Holmer [ [email protected] ], Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden; Ashleigh V.S. Hood [ [email protected] ], School of Geography, Earth and Atmospheric Sciences, University of Melbourne, Parkville, Victoria 3010, Australia; Alexey P. Ippolitov [ [email protected]] , School of Geography, Environment and Earth Sciences, Victoria University of Wellington | Te Herenga Waka, 21 Kelburn Parade, Wellington 6012, New Zealand; Christine M. Janis [ [email protected] ], Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Wills Memorial Building, Bristol, BS8 1RJ, U.K.; Benjamin P. Kear [ [email protected] ], The Museum of Evolution, Uppsala University, Norbyvägen 16, SE-752 36 Uppsala, Sweden; Sophie Kelly [ [email protected] ], School of Earth and Environment, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Justin L. Kitchener [ [email protected] ], School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia; John R. Laurie [ [email protected] ], Geoscience Australia, Symonston, Australian Capital Territory 2601, and School of Natural Sciences, Macquarie University, North Ryde, New South Wales 2109, Australia; Lucy G. Leahey [ [email protected] ], The University of Queensland, Brisbane, Queensland 4072, Australia; John A. Long [ [email protected] ], College of Science and Engineering, Flinders University, PO Box 2100, Adelaide, South Australia 5001, Australia; Daniel Mantle [ [email protected] ], MGPalaeo, Unit 1, 5 Arvida Street, Malaga, Western Australia 6090, Australia; David McB. Martin [ [email protected] ], Geological Survey of Western Australia, Department of Energy, Mines, Industry Regulation and Safety, 100 Plain St, East Perth, Western Australia 6004, Australia; Chris Mays [ [email protected] ], School of Biological, Earth and Environmental Sciences, Environmental Research Institute, University College Cork, Distillery Fields, Cork T23 N73K, Ireland; Matthew R. McCurry [ [email protected] ], Australian Museum, 1 William St, Sydney, New South Wales 2010, Australia; Peter McGoldrick [ [email protected] ], CODES, University of Tasmania, Locked Bag 66, Hobart, Tasmania 7001, Australia; Corinne L. Mensforth [ [email protected] ], Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia; Rhys D. Meyerkort [ [email protected] ], University of Western Australia, 35 Stirling Hwy, Crawley, Western Australia 6009, Australia; Christina Nielsen-Smith [ [email protected] ], School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia; Ryan Nel [ [email protected] ], Geology Department, Rhodes University, Grahamstown, South Africa; Jake Newman-Martin [ [email protected] ], Curtin University, Kent St, Bentley, Western Australia 6102, Australia; Yeongju Oh [ [email protected] ], Division of Earth Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, 21990 Incheon, Republic of Korea, and Polar Science, University of Science and Technology, Daejeon, 34113, Republic of Korea; John R. Paterson [ [email protected] ], Palaeoscience Research Centre, School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia; Jacob Pears [ [email protected] ], School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, Western Australia 6102, Australia; Stephen F. Poropat [ [email protected] ], Western Australian Organic and Isotope Geochemistry Centre, School of Earth and Planetary Science, Curtin University, Kent St, Bentley, Western Australia 6102, and Australian Age of Dinosaurs Museum of Natural History, Winton, Queensland 4735, Australia; Catherine M. Reid [ [email protected] ], School of Earth and Environment, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; R. Pamela Reid [ [email protected] ], Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, U.S.A., and Bahamas Marine EcoCentre, Miami, FL 3315

AusTraits: a curated plant trait database for the Australian flora

INTRODUCTION AusTraits is a transformative database, containing measurements on the traits of Australia’s plant taxa, standardised from hundreds of disconnected primary sources. So far, data have been assembled from > 250 distinct sources, describing > 400 plant traits and > 26,000 taxa. To handle the harmonising of diverse data sources, we use a reproducible workflow to implement the various changes required for each source to reformat it suitable for incorporation in AusTraits. Such changes include restructuring datasets, renaming variables, changing variable units, changing taxon names. While this repository contains the harmonised data, the raw data and code used to build the resource are also available on the project’s GitHub repository, http://traitecoevo.github.io/austraits.build/. Further information on the project is available in the associated publication and at the project website austraits.org. Falster, Gallagher et al (2021) AusTraits, a curated plant trait database for the Australian flora. Scientific Data 8: 254, https://doi.org/10.1038/s41597-021-01006-6 CONTRIBUTORS The project is jointly led by Dr Daniel Falster (UNSW Sydney), Dr Rachael Gallagher (Western Sydney University), Dr Elizabeth Wenk (UNSW Sydney), and Dr Hervé Sauquet (Royal Botanic Gardens and Domain Trust Sydney), with input from > 300 contributors from over > 100 institutions (see full list above). The project was initiated by Dr Rachael Gallagher and Prof Ian Wright while at Macquarie University. We are grateful to the following institutions for contributing data Australian National Botanic Garden, Brisbane Rainforest Action and Information Network, Kew Botanic Gardens, National Herbarium of NSW, Northern Territory Herbarium, Queensland Herbarium, Western Australian Herbarium, South Australian Herbarium, State Herbarium of South Australia, Tasmanian Herbarium, Department of Environment, Land, Water and Planning, Victoria. AusTraits has been supported by investment from the Australian Research Data Commons (ARDC), via their “Transformative data collections” (https://doi.org/10.47486/TD044) and “Data Partnerships” (https://doi.org/10.47486/DP720) programs; fellowship grants from Australian Research Council to Falster (FT160100113), Gallagher (DE170100208) and Wright (FT100100910), a grant from Macquarie University to Gallagher. The ARDC is enabled by National Collaborative Research Investment Strategy (NCRIS). ACCESSING AND USE OF DATA The compiled AusTraits database is released under an open source licence (CC-BY), enabling re-use by the community. A requirement of use is that users cite the AusTraits resource paper, which includes all contributors as co-authors: Falster, Gallagher et al (2021) AusTraits, a curated plant trait database for the Australian flora. Scientific Data 8: 254, https://doi.org/10.1038/s41597-021-01006-6 In addition, we encourage users you to cite the original data sources, wherever possible. Note that under the license data may be redistributed, provided the attribution is maintained. The downloads below provide the data in two formats: austraits-3.0.2.zip: data in plain text format (.csv, .bib, .yml files). Suitable for anyone, including those using Python. austraits-3.0.2.rds: data as compressed R object. Suitable for users of R (see below). Both objects contain all the data and relevant meta-data. AUSTRAITS R PACKAGE For R users, access and manipulation of data is assisted with the austraits R package. The package can both download data and provides examples and functions for running queries. STRUCTURE OF AUSTRAITS The compiled AusTraits database has the following main components: austraits ├── traits ├── sites ├── contexts ├── methods ├── excluded_data ├── taxanomic_updates ├── taxa ├── definitions ├── contributors ├── sources └── build_info These elements include all the data and contextual information submitted with each contributed datasets. A schema and definitions for the database are given in the file/component definitions, available within the download. The file dictionary.html provides the same information in textual format. Full details on each of these components and columns are contained within the definition. Similar information is available at http://traitecoevo.github.io/austraits.build/articles/Trait_definitions.html and http://traitecoevo.github.io/austraits.build/articles/austraits_database_structure.html. CONTRIBUTING We envision AusTraits as an on-going collaborative community resource that: Increases our collective understanding the Australian flora; and Facilitates accumulation and sharing of trait data; Builds a sense of community among contributors and users; and Aspires to fully transparent and reproducible research of the highest standard. As a community resource, we are very keen for people to contribute. Assembly of the database is managed on GitHub at traitecoevo/austraits.build. Here are some of the ways you can contribute: Reporting Errors: If you notice a possible error in AusTraits, please post an issue on GitHub. Refining documentation: We welcome additions and edits that make using the existing data or adding new data easier for the community. Contributing new data: We gladly accept new data contributions to AusTraits. See full instructions on how to contribute at http://traitecoevo.github.io/austraits.build/articles/contributing_data.html