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Article ; Online: GC-MS/FID/EAD

Adam Shuttleworth / Steven D. Johnson

Frontiers in Ecology and Evolution, Vol

A method for combining mass spectrometry with gas chromatography-electroantennographic detection

2022 Volume 10

Abstract: Gas chromatography-electroantennographic detection (GC-EAD), typically combined with a flame ionization detector (FID), is a widely used technique for studying insect semiochemicals. Combining mass spectrometry (MS) with GC-EAD is extremely beneficial, ... ...

Abstract	Gas chromatography-electroantennographic detection (GC-EAD), typically combined with a flame ionization detector (FID), is a widely used technique for studying insect semiochemicals. Combining mass spectrometry (MS) with GC-EAD is extremely beneficial, but has seldom been adopted, possibly due to the practical challenges associated with incorporating an MS (under vacuum) into a GC-EAD system. We describe a novel method of incorporating MS into a GC-EAD system, where the FID is maintained in the system rather than being replaced by an MS. With this method, effluent is still split between EAD and FID, with the FID being used to assign components that elicit antennal responses, as in a normal GC-FID/EAD system. The MS is introduced via a second effluent splitter inserted before the split between the EAD and the FID. This method allows for EAD, FID, and MS data to be obtained from a single injection, which is especially useful for analysis of thermally desorbed and solid-phase microextraction (SPME) samples. This configuration is also relatively simple to implement and resolves some of the practical challenges associated with dividing effluent between a detector at atmospheric pressure (a live antenna) and a detector under vacuum (the MS). We present test runs with hawkmoth antennae and floral volatiles to demonstrate the effectiveness of this system, and discuss the challenges and practical solutions to incorporating MS into a GC-EAD system that retains an FID detector.
Keywords	Electroantennography ; floral volatile ; GC-MS-EAD ; GC-MS/EAD ; GC-FID-EAD ; GC-FID/EAD ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Peer review versus the h-index for evaluation of individual researchers in the biological sciences

Steven D. Johnson

South African Journal of Science, Vol 116, Iss 9/

2020 Volume 10

Abstract: Past performance is a key consideration when rationalising the allocation of grants and other opportunities to individual researchers. The National Research Foundation of South Africa (NRF) has long used a highly structured system of ‘rating’ the past ... ...

Abstract	Past performance is a key consideration when rationalising the allocation of grants and other opportunities to individual researchers. The National Research Foundation of South Africa (NRF) has long used a highly structured system of ‘rating’ the past performance of individual researchers. This system relies heavily on peer review, and has seldom been benchmarked against bibliometric measures of research performance such as Hirsch’s h-index. Here I use data for about 600 rated researchers in the biological sciences to evaluate the extent to which outcomes of peer review correspond to bibliometric measures of research performance. The analysis revealed that values of the h-index based on the Scopus database are typically 5–20 for researchers placed in the NRF’s C rating category (‘established’), 20–40 for those in the B rating category (‘considerable international recognition’) and >40 for those in the A rating category (‘leading international scholars’). Despite concerns that citation patterns differ among disciplines, the mean h-index per rating category was remarkably consistent across five different disciplines in the biological sciences, namely animal sciences, plant sciences, ecology, microbiology and biochemistry/genetics. This observation suggests that the NRF rating system is equitable in the sense that the outcomes of peer review are generally consistent with bibliometric measures of research performance across different disciplines in the biological sciences. However, the study did reveal some notable discrepancies which could reflect either bias in the peer-review process or shortcomings in the bibliometric measures, or both. Significance: • NRF rating categorisations (estimates of standing in a research field based on peer review) are a reasonably good predictor of the h-index of individual researchers in the biological sciences. • The relationships between rating categorisations and the h-index are remarkably consistent across five sub-disciplines in the biological sciences. • Peer review and the ...
Keywords	bibliometrics ; Hirsch’s h-index ; National Research Foundation ; NRF rating ; research administration ; Science ; Q ; Science (General) ; Q1-390 ; Social Sciences ; H ; Social sciences (General) ; H1-99
Subject code	001
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	Academy of Science of South Africa
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Farnesol and phosphorylation of the transcriptional regulator Efg1 affect Candida albicans white-opaque switching rates.

Lucas R Brenes / Alexander D Johnson / Matthew B Lohse

PLoS ONE, Vol 18, Iss 1, p e

2023 Volume 0280233

Abstract: Candida albicans is a normal member of the human microbiome and an opportunistic fungal pathogen. This species undergoes several morphological transitions, and here we consider white-opaque switching. In this switching program, C. albicans reversibly ... ...

Abstract	Candida albicans is a normal member of the human microbiome and an opportunistic fungal pathogen. This species undergoes several morphological transitions, and here we consider white-opaque switching. In this switching program, C. albicans reversibly alternates between two cell types, named "white" and "opaque," each of which is normally stable across thousands of cell divisions. Although switching under most conditions is stochastic and rare, certain environmental signals or genetic manipulations can dramatically increase the rate of switching. Here, we report the identification of two new inputs which affect white-to-opaque switching rates. The first, exposure to sub-micromolar concentrations of (E,E)-farnesol, reduces white-to-opaque switching by ten-fold or more. The second input, an inferred PKA phosphorylation of residue T208 on the transcriptional regulator Efg1, increases white-to-opaque switching ten-fold. Combining these and other environmental inputs results in a variety of different switching rates, indicating that a given rate represents the integration of multiple inputs.
Keywords	Medicine ; R ; Science ; Q
Subject code	420
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effect of fuchsin fixation of pollen on DNA barcode recovery

Melanie B. Streicher / Steven D. Johnson / Sandi Willows‐Munro

Ecology and Evolution, Vol 13, Iss 9, Pp n/a-n/a (2023)

2023

Abstract: Abstract Pollen grains attached to insects are a valuable source of ecological information which can be used to reconstruct visitation networks. Morphological pollen identification relies on light microscopy with pollen usually stained and mounted in ... ...

Abstract	Abstract Pollen grains attached to insects are a valuable source of ecological information which can be used to reconstruct visitation networks. Morphological pollen identification relies on light microscopy with pollen usually stained and mounted in fuchsin jelly, which is also used to remove pollen from the bodies of insects. Pollen embedded in fuchsin jelly could potentially be used for DNA barcoding and metabarcoding (large‐scale taxonomic identification of complex mixed samples) and thus provide additional information for pollination networks. In this study, we determine whether fuchsin‐embedded pollen can be used for downstream molecular applications. We evaluate the quality of plant barcode (ITS) sequences amplified from DNA extracted from both fresh (untreated) pollen, and pollen which had been embedded in fuchsin jelly. We show that the addition of fuchsin to DNA extraction does not impact DNA barcode sequence quality during short‐term storage. DNA extractions from both untreated and fuchsin‐treated pollen produced reliable barcode sequences of high quality. Our findings suggest that pollen which has been collected, stained, and embedded in fuchsin jelly for preliminary microscopy work can be used within several days for downstream genetic analysis, though the quality of DNA from pollen stored in fuchsin jelly for extended periods is yet to be established.
Keywords	barcoding ; fuchsin ; ITS ; pollen identification ; Ecology ; QH540-549.5
Subject code	580 ; 333
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The response of the brood pouch transcriptome to synthetic estrogen exposure in the Gulf pipefish (Syngnathus scovelli)

Emily Rose / Bernadette D. Johnson / Victoria Armitage / Adam G. Jones

Frontiers in Marine Science, Vol

2023 Volume 10

Abstract: Endocrine disruptors have devastating impacts on the reproductive physiology of aquatic organisms. The Gulf pipefish, Syngnathus scovelli, is a sexually dimorphic species, which demonstrates predictable morphological, physiological, behavioral, and ... ...

Abstract	Endocrine disruptors have devastating impacts on the reproductive physiology of aquatic organisms. The Gulf pipefish, Syngnathus scovelli, is a sexually dimorphic species, which demonstrates predictable morphological, physiological, behavioral, and genetic responses to synthetic estrogen exposure. It has a broad geographic range, spanning freshwater and marine environments, making it a potential sentinel species across a wide range of habitats. In this study, we investigated the effects of ecologically relevant levels of 17α-ethinylestradiol (EE2) exposure on gene expression patterns in the male pipefish’s brood pouch. We also characterized the extent to which EE2-exposed males developed coloration patterns that are normally restricted to females. We identified differentially expressed genes in the brood pouches of pregnant and non-pregnant males when males were exposed to 5ng/L EE2 from the second to eighth day of pregnancy (which normally lasts about 2 weeks). Our result revealed several potential candidate genes that have a role in the brood pouch’s response to environmental estrogens. We also identified genes that were differentially expressed between mid-gestation pregnant males and non-pregnant males. We found an overall greater effect of EE2 exposure in the transcriptomes of non-pregnant males, which may explain why estrogen-exposed males exhibited difficulty receiving eggs in previous studies. The offspring developed similarly in the control and estrogen treatments, highlighting a potential link between the timing of EE2 exposure and its effects on male pregnancy. These results provide insight into how breeding pipefish populations may still exist even though they are found in freshwater and coastal locations where they are periodically exposed to potentially high concentrations of endocrine-disrupting compounds. We also present examples of female-typical coloration development on males due to EE2 exposure and identify candidate brood pouch genes that can be utilized as biomarkers, contributing to the ...
Keywords	syngnathidae ; synthetic estrogen ; brood pouch ; transcriptomics ; male pregnancy ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	590
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Confounds and overestimations in fake review detection

Felix Soldner / Bennett Kleinberg / Shane D Johnson

PLoS ONE, Vol 17, Iss 12, p e

Experimentally controlling for product-ownership and data-origin.

2022 Volume 0277869

Abstract: The popularity of online shopping is steadily increasing. At the same time, fake product reviews are published widely and have the potential to affect consumer purchasing behavior. In response, previous work has developed automated methods utilizing ... ...

Abstract	The popularity of online shopping is steadily increasing. At the same time, fake product reviews are published widely and have the potential to affect consumer purchasing behavior. In response, previous work has developed automated methods utilizing natural language processing approaches to detect fake product reviews. However, studies vary considerably in how well they succeed in detecting deceptive reviews, and the reasons for such differences are unclear. A contributing factor may be the multitude of strategies used to collect data, introducing potential confounds which affect detection performance. Two possible confounds are data-origin (i.e., the dataset is composed of more than one source) and product ownership (i.e., reviews written by individuals who own or do not own the reviewed product). In the present study, we investigate the effect of both confounds for fake review detection. Using an experimental design, we manipulate data-origin, product ownership, review polarity, and veracity. Supervised learning analysis suggests that review veracity (60.26-69.87%) is somewhat detectable but reviews additionally confounded with product-ownership (66.19-74.17%), or with data-origin (84.44-86.94%) are easier to classify. Review veracity is most easily classified if confounded with product-ownership and data-origin combined (87.78-88.12%). These findings are moderated by review polarity. Overall, our findings suggest that detection accuracy may have been overestimated in previous studies, provide possible explanations as to why, and indicate how future studies might be designed to provide less biased estimates of detection accuracy.
Keywords	Medicine ; R ; Science ; Q
Subject code	306
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Confounds and overestimations in fake review detection

Felix Soldner / Bennett Kleinberg / Shane D. Johnson

PLoS ONE, Vol 17, Iss

Experimentally controlling for product-ownership and data-origin

2022 Volume 12

Abstract	The popularity of online shopping is steadily increasing. At the same time, fake product reviews are published widely and have the potential to affect consumer purchasing behavior. In response, previous work has developed automated methods utilizing natural language processing approaches to detect fake product reviews. However, studies vary considerably in how well they succeed in detecting deceptive reviews, and the reasons for such differences are unclear. A contributing factor may be the multitude of strategies used to collect data, introducing potential confounds which affect detection performance. Two possible confounds are data-origin (i.e., the dataset is composed of more than one source) and product ownership (i.e., reviews written by individuals who own or do not own the reviewed product). In the present study, we investigate the effect of both confounds for fake review detection. Using an experimental design, we manipulate data-origin, product ownership, review polarity, and veracity. Supervised learning analysis suggests that review veracity (60.26–69.87%) is somewhat detectable but reviews additionally confounded with product-ownership (66.19–74.17%), or with data-origin (84.44–86.94%) are easier to classify. Review veracity is most easily classified if confounded with product-ownership and data-origin combined (87.78–88.12%). These findings are moderated by review polarity. Overall, our findings suggest that detection accuracy may have been overestimated in previous studies, provide possible explanations as to why, and indicate how future studies might be designed to provide less biased estimates of detection accuracy.
Keywords	Medicine ; R ; Science ; Q
Subject code	306
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Redefining Quality in Food Supply Chains via the Natural Resource Based View and Convention Theory

Tracy D. Johnson-Hall / David C. Hall

Sustainability, Vol 14, Iss 9456, p

2022 Volume 9456

Abstract: This study develops and tests a novel product quality framework for food supply chains (FSCs) that addresses sustainability. Issues including climate change, population growth, and the resources required by industrialized agriculture, as well as changing ...

Abstract	This study develops and tests a novel product quality framework for food supply chains (FSCs) that addresses sustainability. Issues including climate change, population growth, and the resources required by industrialized agriculture, as well as changing consumer preferences contribute to concerns about the social, ecological, and economic sustainability of FSCs. FSCs, therefore, need to be adapted to address changing supply and demand characteristics. We integrate the natural resource-based view (NRBV) with convention theory (CT) to develop a new set of quality dimensions. Placing social and ecological considerations within the domain of quality management advances theory in two ways. First, while social and ecological considerations are typically peripheral to business models, this framework allows social responsibility and the natural environment to occupy a central place within FSC operations. Second, the framework reflects the fundamentally socially embedded nature of FSCs, including the geographic, historical, and cultural associations of food quality. We then construct a typology of quality conventions and FSCs. We empirically test the typology using a case study methodology with cases from the United States of America (USA). The analysis explores how firms bundle quality conventions across FSCs for competitive advantage. We also find a set of paths through which FSCs transition via exploitation, exploration and organizational ambidexterity to generate competitive advantage, highlighting tradeoffs that may arise as FSCs evolve. These tradeoffs, which relate to maintaining or adapting quality conventions, are practically important because, if not managed appropriately, may result in lower performance and less sustainable FSCs.
Keywords	quality ; sustainable food supply chains ; food safety ; natural resource-based view ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	360
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Using Bayesian Networks to Provide Educational Implications

Jason D. Johnson / Linda Smail / Darryl Corey / Adeeb M. Jarrah

Sustainability, Vol 14, Iss 5897, p

Mobile Learning and Ethnomathematics to Improve Sustainability in Mathematics Education

2022 Volume 5897

Abstract: There are many Western apps that help students strengthen their mathematics skills through learning and game apps. A research project was designed to create an IOS Math App to provide Grade 6 Emirati students with the opportunity to explore mathematics, ... ...

Abstract	There are many Western apps that help students strengthen their mathematics skills through learning and game apps. A research project was designed to create an IOS Math App to provide Grade 6 Emirati students with the opportunity to explore mathematics, then, using Bayesian Networks, to examine the educational implications. The learning app was developed using ethnomathematics modules based on the Emirati culture. Students were required to navigate through several modules to examine various mathematical concepts in algebra and geometry. The survey was written for Grade 6 English language learners. Based on the Bayesian Networks, the findings suggested that if students are allowed to explore mathematics based on familiar cultural norms and practices, students with grades A and C would get higher grades. However, if students are not allowed to explore mathematics in line with their local culture, more students would receive an F grade, while some students with an A grade would get lower grades. Additionally, the findings showed that incorporating cultural elements had a positive change in students’ liking and learning mathematics, even without a mobile device. However, not allowing a mobile device and not allowing culture had an increased negative impact on students’ liking and learning mathematics. The last finding suggested that students valued ethnomathematics examples over a mobile device to learn mathematics. The research findings could help to improve sustainability in mathematics education by promoting ethnomathematics and mobile learning.
Keywords	Bayesian networks ; ethnomathematics ; mobile learning ; UAE ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	370
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Planning for fauna-sensitive road design

Christopher D. Johnson / Tony Matthews / Matthew Burke / Darryl Jones

Frontiers in Environmental Science, Vol

A review

2022 Volume 10

Abstract: Roads can have significant negative impacts on wildlife. Fauna-sensitive road design (FSRD) can alleviate adverse impacts on several species by installing specialised structures, such as wildlife crossing structures. This developing subfield has ... ...

Abstract	Roads can have significant negative impacts on wildlife. Fauna-sensitive road design (FSRD) can alleviate adverse impacts on several species by installing specialised structures, such as wildlife crossing structures. This developing subfield has generally, however, had a limited impact on transportation planning and management. Indeed, most research is focused narrowly on technological solutions, instead of broader policy learnings. This systematic quantitative literature review (SQLR) of international literature sought to identify the biodiversity concerns acknowledged in transport planning policy, as well as the barriers to the adoption of environmental policies within transport planning. Despite considerable literature available on the impacts of roads on wildlife elsewhere, acknowledgement and consideration of both fauna movement and fauna-sensitive road design were limited in road transportation planning research. More broadly, failure to achieve environmental objectives within transport planning occurred primarily as a result of competing sector interests (conflicted knowledge), different political objectives (political interest), and incorrect interpretation of policies. In essence, the results add new layers of understanding to the field of transportation planning and policy, in particular, the gaps in acknowledgement of wildlife movements and the limitations of current fauna-sensitive road design considered. Importantly, the review identified multiple ecological support tools available to transport policy- and decision-makers. Integration of these in road transportation projects could facilitate enhanced uptake and adoption of FSRD measures and thus foster improved sustainability of the transport network.
Keywords	fauna sensitive road design ; environmental impact assessment ; linear transport infrastructure ; road ecology ; transport planning ; sustainable transport network ; Environmental sciences ; GE1-350
Subject code	380 ; 710
Language	English
Publishing date	2022-09-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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