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Article ; Online: Phenomics: conceptualization and importance for plant physiology.

Zavafer, Alonso / Bates, Harvey / Mancilla, Cristian / Ralph, Peter J

2023 Volume 28, Issue 9, Page(s) 1004–1013

Abstract: Phenomics is a relatively new discipline of biology that has been widely applied in several fields, mainly in crop sciences. We reviewed the concepts used in this discipline (particularly for plants) and found a lack of consensus on what defines a ... ...

Abstract	Phenomics is a relatively new discipline of biology that has been widely applied in several fields, mainly in crop sciences. We reviewed the concepts used in this discipline (particularly for plants) and found a lack of consensus on what defines a phenomic study. Furthermore, phenomics has been primarily developed around its technical aspects (operationalization), while the conceptual framework of the actual research lags behind. Each research group has given its own interpretation of this 'omic' and thus unwittingly created a 'conceptual controversy'. Addressing this issue is of particular importance, as the experimental designs and concepts of phenomics are so diverse that it is difficult to compare studies. In this opinion article, we evaluate the conceptual framework of phenomics.
MeSH term(s)	Phenomics ; Phenotype ; Concept Formation ; Plant Physiological Phenomena ; Plants/genetics
Language	English
Publishing date	2023-05-02
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1305448-x
ISSN	1878-4372 ; 1360-1385
ISSN (online)	1878-4372
ISSN	1360-1385
DOI	10.1016/j.tplants.2023.03.023
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Article ; Online: The slow-phase of chlorophyll fluorescence induction curve reflects the electron transport rates of Photosystem II in vivo in Chlorella vulgaris

Bates, Harvey / Zavafer, Alonso / Szabó, Milán / Ralph, Peter J.

J Appl Phycol. 2023 Feb., v. 35, no. 1 p.109-116

2023

Abstract: Ideally methods and parameters to assess photosynthesis in the microalga Chlorella vulgaris must be rapid, non-invasive, accurate, and simple to implement. Methods such as the Quantum Yield of photosynthesis (ϕPₒ or Fᵥ/Fₘ) yield rapid results but do not ... ...

Abstract	Ideally methods and parameters to assess photosynthesis in the microalga Chlorella vulgaris must be rapid, non-invasive, accurate, and simple to implement. Methods such as the Quantum Yield of photosynthesis (ϕPₒ or Fᵥ/Fₘ) yield rapid results but do not reflect the actual electron turnover of PSII (ETRII). Alternatively, methods that calculate ETRII take several minutes to execute, require expensive instrumentation, and manual input. In this work, we describe a method to estimate ETRII in real-time via predictive statistic modelling. This method utilises the Kautsky induction curve and a low-cost chlorophyll a fluorometer. Our model optimises the fit of linear regressions between the normalized fluorescence intensity after Fₘ (named SETR) and ETRII measurements using traditional methods. This allows for an estimation of ETRII in real-time through Kautsky induction curves alone. SETR can then be used as a faster alternative to quenching analysis to determine bioenergetics performance during steady state and can be assessed with any chlorophyll fluorometer capable of measuring the Kautsky induction curve. The SETR parameter allows for a high-throughput and high-resolution assessment of photosynthesis while being non-invasive, having lower production costs, and with lower technical requirements. Furthermore, the biophysical bases of the method are discussed.
Keywords	Chlorella vulgaris ; chlorophyll ; electron transfer ; fluorescence ; instrumentation ; microalgae ; models ; photosystem II
Language	English
Dates of publication	2023-02
Size	p. 109-116.
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	1002324-0
ISSN	1573-5176 ; 0921-8971
ISSN (online)	1573-5176
ISSN	0921-8971
DOI	10.1007/s10811-022-02890-0
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Article ; Online: Real-Time Environmental Monitoring for Aquaculture Using a LoRaWAN-Based IoT Sensor Network.

Bates, Harvey / Pierce, Matthew / Benter, Allen

Sensors (Basel, Switzerland)

2021 Volume 21, Issue 23

Abstract: IoT-enabled devices are making it easier and cheaper than ever to capture in situ environmental data and deliver these data-in the form of graphical visualisations-to farmers in a matter of seconds. In this work we describe an aquaculture focused ... ...

Abstract	IoT-enabled devices are making it easier and cheaper than ever to capture in situ environmental data and deliver these data-in the form of graphical visualisations-to farmers in a matter of seconds. In this work we describe an aquaculture focused environmental monitoring network consisting of LoRaWAN-enabled atmospheric and marine sensors attached to buoys on Clyde River, located on the South Coast of New South Wales, Australia. This sensor network provides oyster farmers operating on the river with the capacity to make informed, accurate and rapid decisions that enhance their ability to respond to adverse environmental events-typically flooding and heat waves. The system represents an end-to-end approach that involves deploying a sensor network, analysing the data, creating visualisations in collaboration with farmers and delivering them to them in real-time via a website known as FarmDecisionTECH®. We compared this network with previously available infrastructure, the results of which demonstrate that an in situ weather station was ∼5 ∘C hotter than the closest available real-time weather station (∼20 km away from Clyde River) during a summertime heat wave. Heat waves can result in oysters dying due to exposure if temperatures rise above 30 ∘C for extended periods of time (such as heat waves), which will mean a loss in income for the farmers; thus, this work stresses the need for accurate in situ monitoring to prevent the loss of oysters through informed farm management practices. Finally, an approach is proposed to present high-dimensional datasets captured from the sensor network to oyster farmers in a clear and informative manner.
MeSH term(s)	Aquaculture ; Environmental Monitoring ; Farms ; Temperature ; Weather
Language	English
Publishing date	2021-11-29
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/s21237963
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Article ; Online: Risk Attenuation and Amplification in the U.S. Opioid Crisis.

Cantor, Robin / Bates, Heather / MacKoul, Claire

Risk analysis : an official publication of the Society for Risk Analysis

2021 Volume 42, Issue 7, Page(s) 1393–1408

Abstract: The evolution of risk identification and ultimately the public and private responses that have become known collectively as the "opioid crisis" is an important case study in risk management due to the reach and magnitude of its impacts. This article ... ...

Abstract	The evolution of risk identification and ultimately the public and private responses that have become known collectively as the "opioid crisis" is an important case study in risk management due to the reach and magnitude of its impacts. This article examines a number of "signals" related to opioid risks using the social amplification of risk framework (SARF) to investigate a limited set of public-sector activities and policy responses. We evaluate whether the SARF presents an effective lens to examine the serious shortcomings of risk management of opioid use, which has a history of risk attenuation and, more recently, evidence of risk amplification. Our goal in this article is limited to addressing "goodness of fit" of the SARF as a descriptive tool. We consider whether the SARF effectively reveals important gaps in public risk management responses for the opioid example and other similarly situated societal risk problems. Applying SARF supports that its suggested relationship between risk signals and inappropriate attenuated public response does generate useful insights into regulatory efficacy for examples of public risk management. Similar such conclusions about inappropriate public responses stemming from the amplification factors are less supported because, in this case, the risk is, and continues to be, large. Overall, we find that the SARF's particular focus on the signaling function of risk information performs best as an organizational aid to study historical information rather than as a predictive tool for determining inappropriate risk management responses.
MeSH term(s)	Analgesics, Opioid ; Humans ; Policy ; Public Sector
Chemical Substances	Analgesics, Opioid
Language	English
Publishing date	2021-10-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	778660-8
ISSN	1539-6924 ; 0272-4332
ISSN (online)	1539-6924
ISSN	0272-4332
DOI	10.1111/risa.13840
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Article: Involving service users to identify research priorities in a UK forensic mental health service.

Aboaja, Anne / Forsyth, Bunny / Bates, Helen / Wood, Robert

BJPsych bulletin

2021 Volume 45, Issue 6, Page(s) 321–326

Abstract: Aims and method: Patient and public involvement (PPI) is a priority for health research. PPI improves the relevance and quality of research. The study aimed to involve service users in identifying research priorities for the service. A two-phase adapted ...

Abstract	Aims and method: Patient and public involvement (PPI) is a priority for health research. PPI improves the relevance and quality of research. The study aimed to involve service users in identifying research priorities for the service. A two-phase adapted Delphi technique was used to generate a list of research topics from service users in secure in-patient mental health settings and on specialist mental health prison wings. Topic content analysis was undertaken. Service users were further consulted, and research themes were ranked in order of priority. Results: Of the eight research themes identified, the three given the highest priority by service users were, in descending order, physical health, future plans and moving on, and causes of illness and crime. Clinical implications: Service users are willing to be involved in setting research priorities for mental health services. Through non-tokenistic PPI, service users can uniquely shape the research agenda of mental health services.
Language	English
Publishing date	2021-02-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2816886-0
ISSN	2056-4708 ; 2056-4694
ISSN (online)	2056-4708
ISSN	2056-4694
DOI	10.1192/bjb.2020.131
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Article ; Online: Characterization of three

Narayanan, Sai / Couger, Brian / Bates, Haley / Gupta, Sushim Kumar / Malayer, Jerry / Ramachandran, Akhilesh

Access microbiology

2023 Volume 5, Issue 6, Page(s) acmi000451

Abstract: Francisella ... ...

Abstract	Francisella tularensis
Language	English
Publishing date	2023-06-14
Publishing country	England
Document type	Journal Article
ISSN	2516-8290
ISSN (online)	2516-8290
DOI	10.1099/acmi.0.000451
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Article ; Online: Data protection: in our patients' hands.

Thomson, L E / Bates, Hlp

Annals of the Royal College of Surgeons of England

2017 Volume 99, Issue 3, Page(s) 250

Language	English
Publishing date	2017-03
Publishing country	England
Document type	Journal Article
ZDB-ID	80044-2
ISSN	1478-7083 ; 0035-8843
ISSN (online)	1478-7083
ISSN	0035-8843
DOI	10.1308/rcsann.2016.0295
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Article: Discriminating Metabolic Health Status in a Cohort of Nursing Students: Protocol for a Cross-Sectional Study.

West, Sarah L / Bates, Holly / Watson, Jessica / Brenner, Ingrid K M

JMIR research protocols

2020 Volume 9, Issue 8, Page(s) e21342

Abstract: Background: Obesity is currently a worldwide health crisis. Nurses are integral members of the primary health care team and have an important role in managing obesity and administering physical activity (PA) for patients. However, research shows that ... ...

Abstract	Background: Obesity is currently a worldwide health crisis. Nurses are integral members of the primary health care team and have an important role in managing obesity and administering physical activity (PA) for patients. However, research shows that nurses tend to be overweight or obese, have poor metabolic health, and do not meet PA recommendations. This is problematic because PA is linked to both physiological and psychological well-being and may also influence how nurses counsel their patients. Nursing students are the next generation of nurses; however, there is limited research examining PA (among other lifestyle factors) and metabolic health in nursing students. Objective: The goal of this research is to examine multiple lifestyle factors (including PA, nutrition, sleep, and stress) and determine whether these factors are associated with metabolic health in full-time undergraduate nursing students. Methods: An estimated 320 nursing students (18 years of age and older) will be assessed for their metabolic health. Metabolic status will be determined by measuring body mass index (BMI), waist-to-hip ratio (WHR), body fat percentage [skinfold measures (FitSystems Inc)], resting blood pressure [automated oscillatory (Omron Healthcare Inc)], and fasting blood glucose (glucometer). Lifestyle factors will also be measured, including PA and sleep [the International Physical Activity Questionnaire (IPAQ) and 7-day accelerometry (wGT3X-BT, Actigraph LLC)], nutrition [3-day diet log (Nutritionist Pro, Axxya Systems)], and stress [the Depression Anxiety Stress Scale, heart rate variability assessments, and salivary cortisol (ELISA, Eagle Biosciences)]. The association between metabolic status and PA, sleep quantity and quality, nutrition, and stress will be examined by linear regression analyses. Differences by year of study in metabolic health status, PA, sleep, nutrition, and stress will be examined by 1-way analyses of variance (ANOVAs). To determine the ability of PA, sleep, nutrition, and stress to discriminate prevalent overweight and obesity or poor metabolic status, logistic regression and receiver operating characteristic (ROC) curves will be constructed. Statistical analyses will be performed in Stata (version 16.1, StataCorp LLC). Results: Based on pilot data, we believe senior nursing students will have worse metabolic health (ie, higher BMI and WHR, increased body fat percentage, higher blood pressure, and increased fasting blood glucose) compared to first-year students. We hypothesize that poor PA participation, poor sleep quantity and quality, increased food intake, poor nutrition, and increased stress will be associated with worse metabolic health in full-time nursing students. The study received funding in February 2020. Due to the coronavirus disease 2019 (COVID-19) pandemic, work on this study has been delayed. We are currently completing our application for institutional research ethics approval. Data collection is projected to begin in January 2021, with data collection and analyses expected to be completed by May 2022. Conclusions: This study will be the first published research to examine the relationship between lifestyle choices and metabolic status in nursing students attending a Canadian institution. More importantly, the results of this study will support the development of an informed intervention that will target the identified lifestyle factors, improving the physiological and mental health and well-being of nursing students. International registered report identifier (irrid): PRR1-10.2196/21342.
Keywords	covid19
Language	English
Publishing date	2020-08-28
Publishing country	Canada
Document type	Journal Article
ZDB-ID	2719222-2
ISSN	1929-0748
ISSN	1929-0748
DOI	10.2196/21342
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Article: The Phenobottle, an open-source photobioreactor platform for environmental simulation

Bates, Harvey / Zavafer, Alonso / Szabó, Milán / Ralph, Peter J

Algal research. 2020 Dec., v. 52

2020

Abstract: Microalgal biotechnologies have great potential for biofuels, bioremediation, food technologies and more recently the production of pharmaceuticals. However, a major obstacle to use microalgae industrially is the optimisation of environmental parameters ... ...

Abstract	Microalgal biotechnologies have great potential for biofuels, bioremediation, food technologies and more recently the production of pharmaceuticals. However, a major obstacle to use microalgae industrially is the optimisation of environmental parameters to the microalgal species of interest (light, CO₂ availability, nutrients, etc.). If one aims to optimise productivity, the use of photobioreactors (PBRs) is essential. However, the restrictive design of the few commercial bioreactors and their elevated costs (> $10,000 USD ea.) prevents their use as a mainstream tool. To propel microalgal research we present the Phenobottle, a fully customizable open-source PBR platform (consisting of hardware and software). As the optimisation of photosynthesis is a central process to increasing the productivity of microalgae, the Phenobottle is equipped with a chlorophyll a fluorometer and growth sensors to probe metabolic performance in near-real time. An introductory guide is provided and the Phenobottle's sensors are benchmarked against commercial instruments using the model green alga Chlorella vulgaris.
Keywords	Chlorella vulgaris ; biofuels ; bioremediation ; carbon dioxide ; chlorophyll ; computer software ; design ; drugs ; environmental factors ; light ; microalgae ; models ; nutrients ; photobioreactors ; photosynthesis ; research
Language	English
Dates of publication	2020-12
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-light
ISSN	2211-9264
DOI	10.1016/j.algal.2020.102105
Database	NAL-Catalogue (AGRICOLA)

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Article: Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum

Hawke, Tahneal / Bates, Hayley / Hand, Suzanne / Archer, Michael / Broome, Linda

PeerJ

2019 Volume 7, Page(s) e6307

Abstract: Background: The Mountain Pygmy-possum (: Goals and methods: Faecal material was analysed to determine if dietary composition differed between individuals in the newly discovered northern population and those in the higher elevation southern ... ...

Abstract	Background: The Mountain Pygmy-possum ( Goals and methods: Faecal material was analysed to determine if dietary composition differed between individuals in the newly discovered northern population and those in the higher elevation southern population, and to examine how diet was influenced by rainfall in the southern population and seasonal changes in resource availability in the northern population. Results and discussion: The diet of Conclusions: Measurable effects of rainfall amount and seasonal variation on the dietary composition suggest that predicted climatic variability will have a significant impact on its diet, potentially impacting its future survival. Findings suggest that it is likely that
Language	English
Publishing date	2019-01-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.6307
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