Faculty of Health and Environmental Sciences

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The research carried out at AUT's Faculty of Health and Environmental Sciences can be broadly defined in three themes:

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Are Rare Plant Species Less Resistant Than Common Ones to Herbivores? A Multi-plant Species Study Using Above- and Below-Ground Generalist Herbivores
(Wiley, 2023-09-05) Bürli, S; Ensslin, A; Kempel, A; Fischer, M
Rare plant species are suggested to be less resistant to herbivores than common species. Their lower apparency and the fact that they often live in isolated populations, resulting in fewer herbivore encounters, might have led to the evolution of reduced defences. Moreover, their frequent lower levels of genetic diversity compared with common species could negatively affect their resistance against enemies. However, the hypothesis that plant resistance depends on plant regional and local rarity, independently of habitat and competitive and growth strategy, lacks evidence. To test this hypothesis, we assessed the performance and preference of one belowground and three aboveground generalist invertebrate herbivores from different taxonomic groups as indicators of plant resistance. Herbivores were fed a total of 62 regionally and locally rare and common plant species from Switzerland. We accounted for differences in a plant's growth and competitive strategy and habitat resource availability. We found that regionally and locally rare and common plant species did not generally differ in their resistance to most generalist herbivores. However, one herbivore species even performed better and preferred locally and regionally common plant species over rarer ones, indicating that common species are not more resistant, but tend to be less resistant. We also found that all herbivore species consistently performed better on competitive and large plant species, although different herbivore species generally preferred and performed better on different plant species. The latter indicates that the use of generalist herbivores as indicators of plant-resistance levels can be misleading. Synthesis: Our results show that rare plant species are not inherently less resistant than common ones to herbivores. Instead, our results suggest that the ability of plants to allocate resources away from defence towards enhancing their competitive ability might have allowed plants to tolerate herbivory, and to become locally and regionally common.
Assessing Gait & Balance in Adults with Mild Balance Impairment: G&B App Reliability and Validity
(MDPI, 2023-12-09) Shafi, Hina; Awan, Waqar Ahmed; Olsen, Sharon; Siddiqi, Furqan Ahmed; Tassadaq, Naureen; Rashid, Usman; Niazi, Imran Khan
Smartphone applications (apps) that utilize embedded inertial sensors have the potential to provide valid and reliable estimations of different balance and gait parameters in older adults with mild balance impairment. This study aimed to assess the reliability, validity, and sensitivity of the Gait&Balance smartphone application (G&B App) for measuring gait and balance in a sample of middle- to older-aged adults with mild balance impairment in Pakistan. Community-dwelling adults over 50 years of age (N = 83, 50 female, range 50–75 years) with a Berg Balance Scale (BBS) score between 46/56 and 54/56 were included in the study. Data collection involved securing a smartphone to the participant’s lumbosacral spine. Participants performed six standardized balance tasks, including four quiet stance tasks and two gait tasks (walking looking straight ahead and walking with head turns). The G&B App collected accelerometry data during these tasks, and the tasks were repeated twice to assess test-retest reliability. The tasks in quiet stance were also recorded with a force plate, a gold-standard technology for measuring postural sway. Additionally, participants completed three clinical measures, the BBS, the Functional Reach Test (FRT), and the Timed Up and Go Test (TUG). Test-retest reliability within the same session was determined using intraclass correlation coefficients (ICCs) and the standard error of measurement (SEM). Validity was evaluated by correlating the G&B App outcomes against both the force plate data and the clinical measures using Pearson’s product-moment correlation coefficients. To assess the G&B App’s sensitivity to differences in balance across tasks and repetitions, one-way repeated measures analyses of variance (ANOVAs) were conducted. During quiet stance, the app demonstrated moderate reliability for steadiness on firm (ICC = 0.72) and compliant surfaces (ICC = 0.75) with eyes closed. For gait tasks, the G&B App indicated moderate to excellent reliability when walking looking straight ahead for gait symmetry (ICC = 0.65), walking speed (ICC = 0.93), step length (ICC = 0.94), and step time (ICC = 0.84). The TUG correlated with app measures under both gait conditions for walking speed (r −0.70 and 0.67), step length (r −0.56 and −0.58), and step time (r 0.58 and 0.50). The BBS correlated with app measures of walking speed under both gait conditions (r 0.55 and 0.51) and step length when walking with head turns (r = 0.53). Force plate measures of total distance wandered showed adequate to excellent correlations with G&B App measures of steadiness. Notably, G&B App measures of walking speed, gait symmetry, step length, and step time, were sensitive to detecting differences in performance between standard walking and the more difficult task of walking with head turns. This study demonstrates the G&B App’s potential as a reliable and valid tool for assessing some gait and balance parameters in middle-to-older age adults, with promise for application in low-income countries like Pakistan. The app’s accessibility and accuracy could enhance healthcare services and support preventive measures related to fall risk.
Bioluminescence in Cephalopods: Biodiversity, Biogeography and Research Trends
(Frontiers Media SA, 2023-06-27) Otjacques, E; Pissarra, V; Bolstad, K; Xavier, JC; McFall-Ngai, M; Rosa, R
Numerous terrestrial and marine organisms, including cephalopods, are capable of light emission. In addition to communication, bioluminescence is used for attraction and defense mechanisms. The present review aims to: (i) present updated information on the taxonomic diversity of luminous cephalopods and morphological features, (ii) describe large-scale biogeographic patterns, and (iii) show the research trends over the last 50 years on cephalopod bioluminescence. According to our database (834 species), 32% of all known cephalopod species can emit light, including oegopsid and myopsid squids, sepiolids, octopuses, and representatives of several other smaller orders (bathyteuthids, and the monotypic vampire “squid”, Vampyroteuthis infernalis and ram’s horn “squid”, Spirula spirula). Most species have a combination of photophores present in different locations, of which light organs on the head region are dominant, followed by photophores associated with the arms and tentacles and internal photophores. Regarding the biogeographic patterns of cephalopod species with light organs, the most diverse ocean is the Pacific Ocean, followed by the Atlantic and Indian Oceans. The least diverse are the Southern and the Arctic Oceans. Regarding publication trends, our systematic review revealed that, between 1971 and 2020, 277 peer-reviewed studies were published on bioluminescent cephalopods. Most research has been done on a single species, the Hawaiian bobtail squid Euprymna scolopes. The interest in this species is mostly due to its species-specific symbiotic relationship with the bacterium Vibrio fischeri, which is used as a model for the study of Eukaryote–Prokaryote symbiosis. Because there are many knowledge gaps about the biology and biogeography of light-producing cephalopods, new state-of-the-art techniques (e.g., eDNA for diversity research and monitoring) can help achieve a finer resolution on species’ distributions. Moreover, knowledge on the effects of climate change stressors on the bioluminescent processes is nonexistent. Future studies are needed to assess such impacts at different levels of biological organization, to describe the potential broad-scale biogeographic changes, and understand the implications for food web dynamics.
Combining Multiple Stable Isotope Methods Elucidates Diet, Trophic Position and Foraging Areas of Southern Ocean Humpback Whales Megaptera novaeangliae
(Inter-Research Science Center, 2024) Bury, SJ; Peters, KJ; Sabadel, AJM; St. John Glew, K; Trueman, C; Wunder, MB; Cobain, MRD; Schmitt, N; Donnelly, D; Magozzi, S; Owen, K; Brown, JCS; Escobar-Flores, P; Constantine, R; O’Driscoll, RL; Double, M; Gales, N; Childerhouse, S; Pinkerton, MH
Southern Ocean humpback whales Megaptera novaeangliae are capital breeders, breeding in the warm tropics/subtropics in the winter and migrating to nutrient-rich Antarctic feeding grounds in the summer. The classic feeding model is for the species to fast while migrating and breeding, surviving on blubber energy stores. Whilst northern hemisphere humpback whales are generalists, southern hemisphere counterparts are perceived as krill specialists, but for many populations, uncertainties remain regarding their diet and preferred feeding locations. This study used bulk and compound-specific stable isotope analyses and isoscape-based feeding location assignments to assess the diet, trophic ecology and likely feeding areas of humpback whales sampled in the Ross Sea region and around the Balleny Islands. Sampled whales had a mixed diet of plankton, krill and fish, similar to the diet of northern hemisphere humpback whales. Proportions of fish consumed varied but were often high (2-60%), thus challenging the widely held paradigm of Southern Ocean humpback whales being exclusive krill feeders. These whales had lower 15N values and trophic position estimates than their northern hemisphere counterparts, likely due to lower Southern Ocean baseline 15N surface water values and a lower percentage consumption of fish, respectively. Most whales fed in the Ross Sea shelf/slope and Balleny Islands high-productivity regions, but some isotopically distinct whales (mostly males) fed at higher trophic levels either around the Balleny Islands and frontal upwelling areas to the north, or en route to Antarctica in temperate waters off southern Australia and New Zealand. These results support other observations of humpback whales feeding during migration, highlighting the species’ dietary plasticity, which may increase their foraging and breeding success and provide them with greater resilience to anthropogenically mediated ecological change. This study highlights the importance of combining in situ field data with regional-scale isoscapes to reliably assess trophic structure and animal feeding locations, and to better inform ecosystem conservation and management of marine protected areas.
Decoding Attempted Hand Movements in Stroke Patients Using Surface Electromyography
(MDPI AG, 2020-11-26) Jochumsen, M; Niazi, IK; Rehman, MZU; Amjad, I; Shafique, M; Gilani, SO; Waris, A
Brain‐ and muscle‐triggered exoskeletons have been proposed as a means for motor training after a stroke. With the possibility of performing different movement types with an exoskeleton, it is possible to introduce task variability in training. It is difficult to decode different movement types simultaneously from brain activity, but it may be possible from residual muscle activity that many patients have or quickly regain. This study investigates whether nine different motion classes of the hand and forearm could be decoded from forearm EMG in 15 stroke patients. This study also evaluates the test‐retest reliability of a classical, but simple, classifier (linear discriminant analysis) and advanced, but more computationally intensive, classifiers (autoencoders and convolutional neural networks). Moreover, the association between the level of motor impairment and classification accuracy was tested. Three channels of surface EMG were recorded during the following motion classes: Hand Close, Hand Open, Wrist Extension, Wrist Flexion, Supination, Pronation, Lateral Grasp, Pinch Grasp, and Rest. Six repetitions of each motion class were performed on two different days. Hudgins time‐domain features were extracted and classified using linear discriminant analysis and autoencoders, and raw EMG was classified with convolutional neural networks. On average, 79 ± 12% and 80 ± 12% (autoencoders) of the movements were correctly classified for days 1 and 2, respectively, with an intraclass correlation coefficient of 0.88. No association was found between the level of motor impairment and classification accuracy (Spearman correlation: 0.24). It was shown that nine motion classes could be decoded from residual EMG, with autoencoders being the best classification approach, and that the results were reliable across days; this may have implications for the development of EMG‐controlled exoskeletons for training in the patient’s home.
Decoding of Ankle Joint Movements in Stroke Patients Using Surface Electromyography
(MDPI AG, 2021-02-24) Noor, A; Waris, A; Gilani, SO; Kashif, AS; Jochumsen, M; Iqbal, J; Niazi, IK
Stroke is a cerebrovascular disease (CVD), which results in hemiplegia, paralysis, or death. Conventionally, a stroke patient requires prolonged sessions with physical therapists for the recovery of motor function. Various home-based rehabilitative devices are also available for upper limbs and require minimal or no assistance from a physiotherapist. However, there is no clinically proven device available for functional recovery of a lower limb. In this study, we explored the potential use of surface electromyography (sEMG) as a controlling mechanism for the development of a home-based lower limb rehabilitative device for stroke patients. In this experiment, three channels of sEMG were used to record data from 11 stroke patients while performing ankle joint movements. The movements were then decoded from the sEMG data and their correlation with the level of motor impairment was investigated. The impairment level was quantified using the Fugl-Meyer Assessment (FMA) scale. During the analysis, Hudgins time-domain features were extracted and classified using linear discriminant analysis (LDA) and artificial neural network (ANN). On average, 63.86% ± 4.3% and 67.1% ± 7.9% of the movements were accurately classified in an offline analysis by LDA and ANN, respectively. We found that in both classifiers, some motions outperformed oth-ers (p < 0.001 for LDA and p = 0.014 for ANN). The Spearman correlation (ρ) was calculated between the FMA scores and classification accuracies. The results indicate that there is a moderately positive correlation (ρ = 0.75 for LDA and ρ = 0.55 for ANN) between the two of them. The findings of this study suggest that a home-based EMG system can be developed to provide customized therapy for the improvement of functional lower limb motion in stroke patients.
Detection of Error-Related Potentials in Stroke Patients from EEG Using an Artificial Neural Network
(MDPI AG, 2021-09-18) Usama, N; Niazi, IK; Dremstrup, K; Jochumsen, M
Error-related potentials (ErrPs) have been proposed as a means for improving brain– computer interface (BCI) performance by either correcting an incorrect action performed by the BCI or label data for continuous adaptation of the BCI to improve the performance. The latter approach could be relevant within stroke rehabilitation where BCI calibration time could be minimized by using a generalized classifier that is continuously being individualized throughout the rehabilitation session. This may be achieved if data are correctly labelled. Therefore, the aims of this study were: (1) classify single-trial ErrPs produced by individuals with stroke, (2) investigate test–retest reliability, and (3) compare different classifier calibration schemes with different classification methods (artificial neural network, ANN, and linear discriminant analysis, LDA) with waveform features as input for meaningful physiological interpretability. Twenty-five individuals with stroke operated a sham BCI on two separate days where they attempted to perform a movement after which they received feedback (error/correct) while continuous EEG was recorded. The EEG was divided into epochs: ErrPs and NonErrPs. The epochs were classified with a multi-layer perceptron ANN based on temporal features or the entire epoch. Additionally, the features were classified with shrinkage LDA. The features were waveforms of the ErrPs and NonErrPs from the sensorimotor cortex to improve the explainability and interpretation of the output of the classifiers. Three calibration schemes were tested: within-day, between-day, and across-participant. Using within-day calibration, 90% of the data were correctly classified with the entire epoch as input to the ANN; it decreased to 86% and 69% when using temporal features as input to ANN and LDA, respectively. There was poor test–retest reliability between the two days, and the other calibration schemes led to accuracies in the range of 63–72% with LDA performing the best. There was no association between the individuals’ impairment level and classification accuracies. The results show that ErrPs can be classified in individuals with stroke, but that user-and session-specific calibration is needed for optimal ErrP decoding with this approach. The use of ErrP/NonErrP waveform features makes it possible to have a physiological meaningful interpretation of the output of the classifiers. The results may have implications for labelling data continuously in BCIs for stroke rehabilitation and thus potentially improve the BCI performance.
Geometric Implications of Photodiode Arrays on Received Power Distribution in Mobile Underwater Optical Wireless Communication
(MDPI AG, 2024-05-28) Govinda Waduge, Tharuka; Seet, Boon-Chong; Vopel, Kay
Underwater optical wireless communication (UOWC) has gained interest in recent years with the introduction of autonomous and remotely operated mobile systems in blue economic ventures such as offshore food production and energy generation. Here, we devised a model for estimating the received power distribution of diffused line-of-sight mobile optical links, accommodating irregular intensity distributions beyond the beam-spread angle of the emitter. We then used this model to conduct a spatial analysis investigating the parametric influence of the placement, orientation, and angular spread of photodiodes in array-based receivers on the mobile UOWC links in different Jerlov seawater types. It revealed that flat arrays were best for links where strict alignment could be maintained, whereas curved arrays performed better spatially but were not always optimal. Furthermore, utilizing two or more spectrally distinct wavelengths and more bandwidth-efficient modulation may be preferred for received-signal intensity-based localization and improving link range in clearer oceans, respectively. Considering the geometric implications of the array of receiver photodiodes for mobile UOWCs, we recommend the use of dynamically shape-shifting array geometries.
Predicting Ecological Change in Tussock Grasslands of Aotearoa New Zealand
(New Zealand Ecological Society, 2023-11-10) Day, Nicola; Barratt, Barbara; Christensen, Brendon; Curran, Timothy; Dickinson, Katharine; Lavorel, Sandra; Norton, David; Buckley, Hannah
Natural grasslands are among the most threatened biomes on Earth. They are under pressure from land cover change including afforestation, farming intensification, invasive species, altered fire regimes, and soil amendments, all of which impact native biodiversity and ecosystem functioning. In Aotearoa New Zealand, tussock-dominated native grasslands expanded due to increased fire activity during waves of human settlement. These areas have subsequently been maintained as modified grasslands by agricultural pastoral land management practices and effects of introduced feral mammals. Despite many decades of research on biodiversity in tussock grasslands, we need greater fundamental understanding of many processes causing change in their biodiversity and ecosystem functioning in order to predict how future global change will impact this important and increasingly threatened biome. In this perspective forum article, we present five key research questions that, if answered, would greatly enhance our understanding of connections between tussock grassland biodiversity, ecosystem functioning, and associated ecosystem services: (1) What are the relative impacts of domesticated and non-domesticated mammals on indigenous biodiversity in grasslands? (2) Where will invasive plants undergo range expansion? (3) Will future fires tip tussock grasslands into alternative vegetation states? (4) What are the implications of woody thickening by native or non-native species? (5) What are the impacts of global change, and vegetation change in particular, on soil processes and ecosystem functioning? We provide recommendations for research to address and integrate across these questions using both existing and new data. This work would build on our current knowledge and lead to a framework to better understand the ecological impacts of ongoing global change in tussock grasslands.
Priorities for Synthesis Research in Ecology and Environmental Science
(Wiley, 2023-01-11) Halpern, Benjamin S; Boettiger, Carl; Dietze, Michael C; Gephart, Jessica A; Gonzalez, Patrick; Grimm, Nancy B; Groffman, Peter M; Gurevitch, Jessica; Hobbie, Sarah E; Komatsu, Kimberly J; Kroeker, Kristy J; Lahr, Heather J; Lodge, David M; Lortie, Christopher J; Lowndes, Julie SS; Micheli, Fiorenza; Possingham, Hugh P; Ruckelshaus, Mary H; Scarborough, Courtney; Wood, Chelsea L; Wu, Grace C; Aoyama, Lina; Arroyo, Eva E; Bahlai, Christie A; Beller, Erin E; Blake, Rachael E; Bork, Karrigan S; Branch, Trevor A; Brown, Norah EM; Brun, Julien; Bruna, Emilio M; Buckley, Lauren B; Burnett, Jessica L; Castorani, Max CN; Cheng, Samantha H; Cohen, Sarah C; Couture, Jessica L; Crowder, Larry B; Dee, Laura E; Dias, Arildo S; Diaz‐Maroto, Ignacio J; Downs, Martha R; Dudney, Joan C; Ellis, Erle C; Emery, Kyle A; Eurich, Jacob G; Ferriss, Bridget E; Fredston, Alexa; Furukawa, Hikaru; Gagné, Sara A; Garlick, Sarah R; Garroway, Colin J; Gaynor, Kaitlyn M; González, Angélica L; Grames, Eliza M; Guy‐Haim, Tamar; Hackett, Ed; Hallett, Lauren M; Harms, Tamara K; Haulsee, Danielle E; Haynes, Kyle J; Hazen, Elliott L; Jarvis, Rebecca M; Jones, Kristal; Kandlikar, Gaurav S; Kincaid, Dustin W; Knope, Matthew L; Koirala, Anil; Kolasa, Jurek; Kominoski, John S; Koricheva, Julia; Lancaster, Lesley T; Lawlor, Jake A; Lowman, Heili E; Muller‐Karger, Frank E; Norman, Kari EA; Nourn, Nan; O'Hara, Casey C; Ou, Suzanne X; Padilla‐Gamino, Jacqueline L; Pappalardo, Paula; Peek, Ryan A; Pelletier, Dominique; Plont, Stephen; Ponisio, Lauren C; Portales‐Reyes, Cristina; Provete, Diogo B; Raes, Eric J; Ramirez‐Reyes, Carlos; Ramos, Irene; Record, Sydne; Richardson, Anthony J; Salguero‐Gómez, Roberto; Satterthwaite, Erin V; Schmidt, Chloé; Schwartz, Aaron J; See, Craig R; Shea, Brendan D; Smith, Rachel S; Sokol, Eric R; Solomon, Christopher T; Spanbauer, Trisha; Stefanoudis, Paris V; Sterner, Beckett W; Sudbrack, Vitor; Tonkin, Jonathan D; Townes, Ashley R; Valle, Mireia; Walter, Jonathan A; Wheeler, Kathryn I; Wieder, William R; Williams, David R; Winter, Marten; Winterova, Barbora; Woodall, Lucy C; Wymore, Adam S; Youngflesh, Casey
Synthesis research in ecology and environmental science improves understanding, advances theory, identifies research priorities, and supports management strategies by linking data, ideas, and tools. Accelerating environmental challenges increases the need to focus synthesis science on the most pressing questions. To leverage input from the broader research community, we convened a virtual workshop with participants from many countries and disciplines to examine how and where synthesis can address key questions and themes in ecology and environmental science in the coming decade. Seven priority research topics emerged: (1) diversity, equity, inclusion, and justice (DEIJ), (2) human and natural systems, (3) actionable and use-inspired science, (4) scale, (5) generality, (6) complexity and resilience, and (7) predictability. Additionally, two issues regarding the general practice of synthesis emerged: the need for increased participant diversity and inclusive research practices; and increased and improved data flow, access, and skill-building. These topics and practices provide a strategic vision for future synthesis in ecology and environmental science.
Rarity and Life-History Strategies Shape Inbreeding and Outbreeding Effects on Early Plant Fitness
(Elsevier BV, 2024-10) Bürli, Sarah; Ensslin, Andreas; Fischer, Markus
Local abundance and regional distribution are two aspects of a species’ rarity. They are suggested to differentially alter genetic processes in plants: Locally rare species are hypothesized to suffer less from inbreeding and outbreeding than locally common species, thanks to genetic purging through long inbreeding histories and weaker local adaptations, respectively. Regionally rare species are hypothesized to be more susceptible to outbreeding, but less to inbreeding, compared to regionally common ones, due to small and declining range size. While this has major implications for plant conservation practices, we lack evidences and general understanding on how breeding effects on a plant’s early life fitness are related to its local and regional rarity. To investigate effects of inbreeding and outbreeding on plants’ early fitness, we performed self-, within- and between-population pollinations in eight pairs of closely related species differing in regional and local rarity. To avoid biases due to context dependency, we took species competitive ability, habitat resource-richness and resource-allocation strategy into account in the analyses. We then tested how inbreeding and outbreeding affected five fruit-, seed- and seedling-related traits. Inbreeding did not generally have more negative effects on early fitness of regionally rare and non-competitive species than on regionally common and competitive ones. Outbreeding was generally beneficial to early fitness of plant species across the gradients of regional rarity, competitive ability and habitat resource-richness. Our results show that outbreeding may be beneficial to the early fitness of plant species, including rare and non-competitive ones and may be considered for conservation strategies.
Single-Trial Classification of Error-Related Potentials in People with Motor Disabilities: A Study in Cerebral Palsy, Stroke, and Amputees
(MDPI AG, 2022-02-21) Usama, N; Niazi, IK; Dremstrup, K; Jochumsen, M
Brain-computer interface performance may be reduced over time, but adapting the classifier could reduce this problem. Error-related potentials (ErrPs) could label data for continuous adaptation. However, this has scarcely been investigated in populations with severe motor impairments. The aim of this study was to detect ErrPs from single-trial EEG in offline analysis in participants with cerebral palsy, an amputation, or stroke, and determine how much discriminative information different brain regions hold. Ten participants with cerebral palsy, eight with an amputation, and 25 with a stroke attempted to perform 300–400 wrist and ankle movements while a sham BCI provided feedback on their performance for eliciting ErrPs. Pre-processed EEG epochs were inputted in a multi-layer perceptron artificial neural network. Each brain region was used as input individually (Frontal, Central, Temporal Right, Temporal Left, Parietal, and Occipital), the combination of the Central region with each of the adjacent regions, and all regions combined. The Frontal and Central regions were most important, and adding additional regions only improved performance slightly. The average classification accuracies were 84 ± 4%, 87± 4%, and 85 ± 3% for cerebral palsy, amputation, and stroke participants. In conclusion, ErrPs can be detected in participants with motor impairments; this may have implications for developing adaptive BCIs or automatic error correction.

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