PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Measurement of lower-limb asymmetry in professional rugby league: a technical note describing the use of inertial measurement units
items: Assessing bias in demographic estimates from joint live and dead encounter models
items: Lateralized alpha oscillations are irrelevant for the behavioral retro-cueing benefit in visual working memory
items: Modelling fatality curves of COVID-19 and the effectiveness of intervention strategies
items: Biochemical and toxicological effects of methanolic extract of Asparagus africanus Lam in Sprague-Dawley rats
items: Organic eutrophication increases resistance of the pulsating soft coral Xenia umbellata to warming
items: A game-theoretic model of Monkeypox to assess vaccination strategies
items: Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants
items: A revision of the pelomedusoid turtle Jainemys pisdurensis from the Late Cretaceous (Maastrichtian) Lameta Formation of India
items: Salticidae (Arachnida, Araneae) of Thailand: new species and records of Epeus Peckham & Peckham, 1886 and Ptocasius Simon, 1885

Measurement of lower-limb asymmetry in professional rugby league: a technical note describing the use of inertial measurement units
type: item
type: AcademicArticle
description: Background Quantifying lower-limb load and asymmetry during team sport match-play may be important for injury prevention and understanding performance. However, current analysis methods of lower-limb symmetry during match-play employ wearable microtechnology that may not be best suited to the task. A popular microtechnology is global positioning systems (GPS), which are torso worn. The torso location, and the summary workload measures calculated by GPS are not suited to the calculation of lower-limb load. Instead, research grade accelerometers placed directly on the lower-limb may provide better load information than GPS. This study proposes a new technique to quantify external mechanical load, and lower-limb asymmetry during on-field team sport play using inertial measurement units. Methods Four professional rugby league players (Age: 23.4 ± 3.1 years; Height: 1.89 ± 0.05 m; Mass: 107.0 ± 12.9 kg) wore two accelerometers, one attached to each foot by the boot laces, during match simulations. Custom Matlab (R2017b, The Mathworks Inc, Natick, MA) code was used to calculate total time, area under the curve (AUC), and percentage of time (%Time) spent in seven acceleration categories (negative to very high, <0 g to >16 g), as well as minimum and maximum acceleration during match simulations. Lower-limb AUC and %Time asymmetry was calculated using the Symmetry Angle Equation, which does not require normalization to a reference leg. Results The range of accelerations experienced across all participants on the left and right sides were 15.68–17.53 g, and 16.18–17.69 g, respectively. Clinically significant asymmetry in AUC and %Time was observed for all but one participant, and only in negative (<0 g) and very high accelerations (>16 g). Clinically significant AUC differences in very high accelerations ranged from 19.10%–26.71%. Clinically significant %Time differences in negative accelerations ranged from 12.65%–25.14%, and in very high accelerations from 18.59%–25.30%. Al…
format: application/pdf
format: text/html
creator: Daniel J. Glassbrook
creator: Joel T. Fuller
creator: Jacqueline A. Alderson
creator: Tim L.A. Doyle
subject: Bioengineering
subject: Anatomy and Physiology
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.9366
publisher: PeerJ Inc.
rights: © 2020 Glassbrook et al.
abstract: Background Quantifying lower-limb load and asymmetry during team sport match-play may be important for injury prevention and understanding performance. However, current analysis methods of lower-limb symmetry during match-play employ wearable microtechnology that may not be best suited to the task. A popular microtechnology is global positioning systems (GPS), which are torso worn. The torso location, and the summary workload measures calculated by GPS are not suited to the calculation of lower-limb load. Instead, research grade accelerometers placed directly on the lower-limb may provide better load information than GPS. This study proposes a new technique to quantify external mechanical load, and lower-limb asymmetry during on-field team sport play using inertial measurement units. Methods Four professional rugby league players (Age: 23.4 ± 3.1 years; Height: 1.89 ± 0.05 m; Mass: 107.0 ± 12.9 kg) wore two accelerometers, one attached to each foot by the boot laces, during match simulations. Custom Matlab (R2017b, The Mathworks Inc, Natick, MA) code was used to calculate total time, area under the curve (AUC), and percentage of time (%Time) spent in seven acceleration categories (negative to very high, <0 g to >16 g), as well as minimum and maximum acceleration during match simulations. Lower-limb AUC and %Time asymmetry was calculated using the Symmetry Angle Equation, which does not require normalization to a reference leg. Results The range of accelerations experienced across all participants on the left and right sides were 15.68–17.53 g, and 16.18–17.69 g, respectively. Clinically significant asymmetry in AUC and %Time was observed for all but one participant, and only in negative (<0 g) and very high accelerations (>16 g). Clinically significant AUC differences in very high accelerations ranged from 19.10%–26.71%. Clinically significant %Time differences in negative accelerations ranged from 12.65%–25.14%, and in very high accelerations from 18.59%–25.30%. Al…
bibliographic citation: Glassbrook et al. (2020) Measurement of lower-limb asymmetry in professional rugby league: a technical note describing the use of inertial measurement units. PeerJ 8:e9366 https://doi.org/10.7717/peerj.9366
date submitted: 2020-04-08
date accepted: 2020-05-26
issued: 2020-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Glassbrook
  given name: Daniel J.
author list: Agent
  family name: Fuller
  given name: Joel T.
author list: Agent
  family name: Alderson
  given name: Jacqueline A.
author list: Agent
  family name: Doyle
  given name: Tim L.A.
doi: 10.7717/peerj.9366
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-23
copyright: ©2020 Glassbrook et al.
attribution name: Glassbrook et al.

Assessing bias in demographic estimates from joint live and dead encounter models
type: item
type: AcademicArticle
description: Joint encounter (JE) models estimate demographic rates using live recapture and dead recovery data. The extent to which limited recapture or recovery data can hinder estimation in JE models is not completely understood. Yet limited data are common in ecological research. We designed a series of simulations using Bayesian multistate JE models that spanned a large range of potential recapture probabilities (0.01–0.90) and two reported mortality probabilities (0.10, 0.19). We calculated bias by comparing estimates against known probabilities of survival, fidelity and reported mortality. We explored whether sparse data (i.e., recapture probabilities <0.02) compromised inference about survival by comparing estimates from dead recovery (DR) and JE models using an 18-year data set from a migratory bird, the lesser snow goose (Anser caerulescens caerulescens). Our simulations showed that bias in probabilities of survival, fidelity and reported mortality was relatively low across a large range of recapture probabilities, except when recapture and reported mortality probabilities were both lowest. While bias in fidelity probability was similar across all recapture probabilities, the root mean square error declined substantially with increased recapture probabilities for reported mortality probabilities of 0.10 or 0.19, as expected. In our case study, annual survival probabilities for adult female snow geese were similar whether estimated with JE or DR models, but more precise from JE models than those from DR models. Thus, our simulated and empirical data suggest acceptably minimal bias in survival, fidelity or reported mortality probabilities estimated from JE models. Even a small amount of recapture information provided adequate structure for JE models, except when reported mortality probabilities were <0.10. Thus, practitioners with limited recapture data should not be discouraged from use of JE models. We recommend that ecologists incorporate other data types as frequentl…
format: application/pdf
format: text/html
creator: Mitch D. Weegman
creator: Scott Wilson
creator: Ray T. Alisauskas
creator: Dana K. Kellett
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.9382
publisher: PeerJ Inc.
rights: © 2020 Weegman et al.
abstract: Joint encounter (JE) models estimate demographic rates using live recapture and dead recovery data. The extent to which limited recapture or recovery data can hinder estimation in JE models is not completely understood. Yet limited data are common in ecological research. We designed a series of simulations using Bayesian multistate JE models that spanned a large range of potential recapture probabilities (0.01–0.90) and two reported mortality probabilities (0.10, 0.19). We calculated bias by comparing estimates against known probabilities of survival, fidelity and reported mortality. We explored whether sparse data (i.e., recapture probabilities <0.02) compromised inference about survival by comparing estimates from dead recovery (DR) and JE models using an 18-year data set from a migratory bird, the lesser snow goose (Anser caerulescens caerulescens). Our simulations showed that bias in probabilities of survival, fidelity and reported mortality was relatively low across a large range of recapture probabilities, except when recapture and reported mortality probabilities were both lowest. While bias in fidelity probability was similar across all recapture probabilities, the root mean square error declined substantially with increased recapture probabilities for reported mortality probabilities of 0.10 or 0.19, as expected. In our case study, annual survival probabilities for adult female snow geese were similar whether estimated with JE or DR models, but more precise from JE models than those from DR models. Thus, our simulated and empirical data suggest acceptably minimal bias in survival, fidelity or reported mortality probabilities estimated from JE models. Even a small amount of recapture information provided adequate structure for JE models, except when reported mortality probabilities were <0.10. Thus, practitioners with limited recapture data should not be discouraged from use of JE models. We recommend that ecologists incorporate other data types as frequentl…
bibliographic citation: Weegman et al. (2020) Assessing bias in demographic estimates from joint live and dead encounter models. PeerJ 8:e9382 https://doi.org/10.7717/peerj.9382
date submitted: 2020-02-13
date accepted: 2020-05-28
issued: 2020-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weegman
  given name: Mitch D.
author list: Agent
  family name: Wilson
  given name: Scott
author list: Agent
  family name: Alisauskas
  given name: Ray T.
author list: Agent
  family name: Kellett
  given name: Dana K.
doi: 10.7717/peerj.9382
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-23
copyright: © 2020 Weegman et al.
attribution name: Weegman et al.

Lateralized alpha oscillations are irrelevant for the behavioral retro-cueing benefit in visual working memory
type: item
type: AcademicArticle
description: The limited capacity of visual working memory (vWM) necessitates the efficient allocation of available resources by prioritizing relevant over irrelevant items. Retro-cues, which inform about the future relevance of items after encoding has already finished, can improve the quality of memory representations of the relevant items. A candidate mechanism of this retro-cueing benefit is lateralization of neural oscillations in the alpha-band, but its precise role is still debated. The relative decrease of alpha power contralateral to the relevant items has been interpreted as supporting inhibition of irrelevant distractors or as supporting maintenance of relevant items. Here, we aimed at resolving this debate by testing how the magnitude of alpha-band lateralization affects behavioral performance: does stronger lateralization improve the precision of the relevant memory or does it reduce the biasing influence of the irrelevant distractor? We found that it does neither: while the data showed a clear retro-cue benefit and a biasing influence of non-target items as well as clear cue-induced alpha-band lateralization, the magnitude of this lateralization was not correlated with any performance parameter. This finding may indicate that alpha-band lateralization, which is typically observed in response to mnemonic cues, indicates an automatic shift of attention that only coincides with, but is not directly involved in mnemonic prioritization.
format: application/pdf
format: text/html
creator: Wanja A. Mössing
creator: Niko A. Busch
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9398
publisher: PeerJ Inc.
rights: © 2020 Mössing and Busch
abstract: The limited capacity of visual working memory (vWM) necessitates the efficient allocation of available resources by prioritizing relevant over irrelevant items. Retro-cues, which inform about the future relevance of items after encoding has already finished, can improve the quality of memory representations of the relevant items. A candidate mechanism of this retro-cueing benefit is lateralization of neural oscillations in the alpha-band, but its precise role is still debated. The relative decrease of alpha power contralateral to the relevant items has been interpreted as supporting inhibition of irrelevant distractors or as supporting maintenance of relevant items. Here, we aimed at resolving this debate by testing how the magnitude of alpha-band lateralization affects behavioral performance: does stronger lateralization improve the precision of the relevant memory or does it reduce the biasing influence of the irrelevant distractor? We found that it does neither: while the data showed a clear retro-cue benefit and a biasing influence of non-target items as well as clear cue-induced alpha-band lateralization, the magnitude of this lateralization was not correlated with any performance parameter. This finding may indicate that alpha-band lateralization, which is typically observed in response to mnemonic cues, indicates an automatic shift of attention that only coincides with, but is not directly involved in mnemonic prioritization.
bibliographic citation: Mössing et al. (2020) Lateralized alpha oscillations are irrelevant for the behavioral retro-cueing benefit in visual working memory. PeerJ 8:e9398 https://doi.org/10.7717/peerj.9398
date submitted: 2020-02-19
date accepted: 2020-05-30
issued: 2020-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mössing
  given name: Wanja A.
author list: Agent
  family name: Busch
  given name: Niko A.
doi: 10.7717/peerj.9398
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-23
copyright: © 2020 Mössing and Busch
attribution name: Mössing and Busch

Modelling fatality curves of COVID-19 and the effectiveness of intervention strategies
type: item
type: AcademicArticle
description: The main objective of the present article is twofold: first, to model the fatality curves of the COVID-19 disease, as represented by the cumulative number of deaths as a function of time; and second, to use the corresponding mathematical model to study the effectiveness of possible intervention strategies. We applied the Richards growth model (RGM) to the COVID-19 fatality curves from several countries, where we used the data from the Johns Hopkins University database up to May 8, 2020. Countries selected for analysis with the RGM were China, France, Germany, Iran, Italy, South Korea, and Spain. The RGM was shown to describe very well the fatality curves of China, which is in a late stage of the COVID-19 outbreak, as well as of the other above countries, which supposedly are in the middle or towards the end of the outbreak at the time of this writing. We also analysed the case of Brazil, which is in an initial sub-exponential growth regime, and so we used the generalised growth model which is more appropriate for such cases. An analytic formula for the efficiency of intervention strategies within the context of the RGM is derived. Our findings show that there is only a narrow window of opportunity, after the onset of the epidemic, during which effective countermeasures can be taken. We applied our intervention model to the COVID-19 fatality curve of Italy of the outbreak to illustrate the effect of several possible interventions.
format: application/pdf
format: text/html
creator: Giovani L. Vasconcelos
creator: Antônio M.S. Macêdo
creator: Raydonal Ospina
creator: Francisco A.G. Almeida
creator: Gerson C. Duarte-Filho
creator: Arthur A. Brum
creator: Inês C.L. Souza
subject: Mathematical Biology
subject: Epidemiology
subject: Global Health
description: doi:10.7717/peerj.9421
publisher: PeerJ Inc.
rights: © 2020 Vasconcelos et al.
abstract: The main objective of the present article is twofold: first, to model the fatality curves of the COVID-19 disease, as represented by the cumulative number of deaths as a function of time; and second, to use the corresponding mathematical model to study the effectiveness of possible intervention strategies. We applied the Richards growth model (RGM) to the COVID-19 fatality curves from several countries, where we used the data from the Johns Hopkins University database up to May 8, 2020. Countries selected for analysis with the RGM were China, France, Germany, Iran, Italy, South Korea, and Spain. The RGM was shown to describe very well the fatality curves of China, which is in a late stage of the COVID-19 outbreak, as well as of the other above countries, which supposedly are in the middle or towards the end of the outbreak at the time of this writing. We also analysed the case of Brazil, which is in an initial sub-exponential growth regime, and so we used the generalised growth model which is more appropriate for such cases. An analytic formula for the efficiency of intervention strategies within the context of the RGM is derived. Our findings show that there is only a narrow window of opportunity, after the onset of the epidemic, during which effective countermeasures can be taken. We applied our intervention model to the COVID-19 fatality curve of Italy of the outbreak to illustrate the effect of several possible interventions.
bibliographic citation: Vasconcelos et al. (2020) Modelling fatality curves of COVID-19 and the effectiveness of intervention strategies. PeerJ 8:e9421 https://doi.org/10.7717/peerj.9421
date submitted: 2020-04-04
date accepted: 2020-06-04
issued: 2020-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vasconcelos
  given name: Giovani L.
author list: Agent
  family name: Macêdo
  given name: Antônio M.S.
author list: Agent
  family name: Ospina
  given name: Raydonal
author list: Agent
  family name: Almeida
  given name: Francisco A.G.
author list: Agent
  family name: Duarte-Filho
  given name: Gerson C.
author list: Agent
  family name: Brum
  given name: Arthur A.
author list: Agent
  family name: Souza
  given name: Inês C.L.
doi: 10.7717/peerj.9421
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-23
copyright: © 2020 Vasconcelos et al.
attribution name: Vasconcelos et al.

Biochemical and toxicological effects of methanolic extract of Asparagus africanus Lam in Sprague-Dawley rats
type: item
type: AcademicArticle
description: Asparagus africanus Lam. is a plant used traditionally to treat different ailments. Currently, scanty information is available on its safety. The aim of this study is to determine the acute toxicity of the methanolic extract on vital organs and its associated biochemical parameters. Fifteen female Sprague-Dawley rats were divided into five groups. Group I served as normal control, groups II, III, IV, and V were orally administered single dose of crude extract dissolved in distilled water at 5 mg/kg BW, 50 mg/kg BW, 300 mg/kg BW and 2,000 mg/kg BW. Rats were observed for 14 days and body weights were recorded. On day 15, the rats were sacrificed and blood samples were collected for biochemical and haematological analyses, while the liver and kidneys were sampled for histopathological examination. Body weight and haematology parameters results showed significance difference (p < 0.05) among means of HGB, RDW, RBC, and MCHC; likewise, (p < 0.001) for WBC and platelet among treated groups. Histopathology result showed that kidneys appeared normal while livers were congested with mildly swollen hepatocytes and occasional binucleation. Focal lobular hepatitis was observed in all treated animals. However, hepatic enzymes were not significantly affected and no histopathological harmful effects were observed in kidney. In conclusion, methanolic extracts of A. africanus are safe up to 2,000 mg/kg BW. The obtained results could be used as a justification for the traditional application of the plant for treatment of various ailments.
format: application/pdf
format: text/html
creator: Abubakar El-Ishaq
creator: Mohammed A. Alshawsh
creator: Kein Seong Mun
creator: Zamri Chik
subject: Biochemistry
subject: Toxicology
subject: Hematology
subject: Pharmacology
description: doi:10.7717/peerj.9138
publisher: PeerJ Inc.
rights: © 2020 El-Ishaq et al.
abstract: Asparagus africanus Lam. is a plant used traditionally to treat different ailments. Currently, scanty information is available on its safety. The aim of this study is to determine the acute toxicity of the methanolic extract on vital organs and its associated biochemical parameters. Fifteen female Sprague-Dawley rats were divided into five groups. Group I served as normal control, groups II, III, IV, and V were orally administered single dose of crude extract dissolved in distilled water at 5 mg/kg BW, 50 mg/kg BW, 300 mg/kg BW and 2,000 mg/kg BW. Rats were observed for 14 days and body weights were recorded. On day 15, the rats were sacrificed and blood samples were collected for biochemical and haematological analyses, while the liver and kidneys were sampled for histopathological examination. Body weight and haematology parameters results showed significance difference (p < 0.05) among means of HGB, RDW, RBC, and MCHC; likewise, (p < 0.001) for WBC and platelet among treated groups. Histopathology result showed that kidneys appeared normal while livers were congested with mildly swollen hepatocytes and occasional binucleation. Focal lobular hepatitis was observed in all treated animals. However, hepatic enzymes were not significantly affected and no histopathological harmful effects were observed in kidney. In conclusion, methanolic extracts of A. africanus are safe up to 2,000 mg/kg BW. The obtained results could be used as a justification for the traditional application of the plant for treatment of various ailments.
bibliographic citation: El-Ishaq et al. (2020) Biochemical and toxicological effects of methanolic extract of Asparagus africanus Lam in Sprague-Dawley rats. PeerJ 8:e9138 https://doi.org/10.7717/peerj.9138
date submitted: 2019-06-19
date accepted: 2020-04-15
issued: 2020-06-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: El-Ishaq
  given name: Abubakar
author list: Agent
  family name: Alshawsh
  given name: Mohammed A.
author list: Agent
  family name: Mun
  given name: Kein Seong
author list: Agent
  family name: Chik
  given name: Zamri
doi: 10.7717/peerj.9138
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-22
copyright: ©2020 El-Ishaq et al.
attribution name: El-Ishaq et al.

Organic eutrophication increases resistance of the pulsating soft coral Xenia umbellata to warming
type: item
type: AcademicArticle
description: Recent research indicates that hard corals in a process that is termed phase shift are often replaced by soft corals in reefs. The simultaneous occurrence of local (i.e. organic eutrophication as highly under-investigated parameter) and global (i.e. ocean warming) factors may facilitate these phase shifts as hard corals are negatively affected by both ocean warming and organic eutrophication. Knowledge about soft coral responses to environmental change remains incomplete, although these organisms are becoming important players in reefs. The present study thus investigated the individual and combined effects of organic eutrophication (as glucose addition) and warming on the ecological data of the pulsating soft coral Xenia umbellata. We assessed health status, growth and pulsation rates of soft corals in a 45 day aquarium experiment, with first manipulation of organic eutrophication (no, low, medium and high glucose addition) over 21 days followed by step-wise increases in water temperature from 26 to 32 °C over 24 days. Findings revealed that glucose addition did not affect health status, growth and pulsation rates of the investigated soft corals. Under simulated ocean warming, soft corals that had experienced organic eutrophication before, maintained significantly higher pulsation rates (averaging 22 beats per minute—bpm) and no mortality compared to the controls that showed a decrease of 56% (averaging 15 bpm) in pulsation rates and mortality of 30% at water temperatures of 32 °C compared to 26 °C. This apparently positive effect of organic eutrophication on the ecological data of soft corals under an ocean warming scenario decreased with increasing water temperature. This study thus indicates that (a) organic eutrophication as additional energy source up to a certain threshold may increase the resistance of soft corals to ocean warming and (b) pulsation rates of soft corals may be used as inexpensive, easily detectable, and non-invasive early warning indicator fo…
format: application/pdf
format: text/html
creator: Svea Vollstedt
creator: Nan Xiang
creator: Susana Marcela Simancas-Giraldo
creator: Christian Wild
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.9182
publisher: PeerJ Inc.
rights: © 2020 Vollstedt et al.
abstract: Recent research indicates that hard corals in a process that is termed phase shift are often replaced by soft corals in reefs. The simultaneous occurrence of local (i.e. organic eutrophication as highly under-investigated parameter) and global (i.e. ocean warming) factors may facilitate these phase shifts as hard corals are negatively affected by both ocean warming and organic eutrophication. Knowledge about soft coral responses to environmental change remains incomplete, although these organisms are becoming important players in reefs. The present study thus investigated the individual and combined effects of organic eutrophication (as glucose addition) and warming on the ecological data of the pulsating soft coral Xenia umbellata. We assessed health status, growth and pulsation rates of soft corals in a 45 day aquarium experiment, with first manipulation of organic eutrophication (no, low, medium and high glucose addition) over 21 days followed by step-wise increases in water temperature from 26 to 32 °C over 24 days. Findings revealed that glucose addition did not affect health status, growth and pulsation rates of the investigated soft corals. Under simulated ocean warming, soft corals that had experienced organic eutrophication before, maintained significantly higher pulsation rates (averaging 22 beats per minute—bpm) and no mortality compared to the controls that showed a decrease of 56% (averaging 15 bpm) in pulsation rates and mortality of 30% at water temperatures of 32 °C compared to 26 °C. This apparently positive effect of organic eutrophication on the ecological data of soft corals under an ocean warming scenario decreased with increasing water temperature. This study thus indicates that (a) organic eutrophication as additional energy source up to a certain threshold may increase the resistance of soft corals to ocean warming and (b) pulsation rates of soft corals may be used as inexpensive, easily detectable, and non-invasive early warning indicator fo…
bibliographic citation: Vollstedt et al. (2020) Organic eutrophication increases resistance of the pulsating soft coral Xenia umbellata to warming. PeerJ 8:e9182 https://doi.org/10.7717/peerj.9182
date submitted: 2019-10-31
date accepted: 2020-04-22
issued: 2020-06-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vollstedt
  given name: Svea
author list: Agent
  family name: Xiang
  given name: Nan
author list: Agent
  family name: Simancas-Giraldo
  given name: Susana Marcela
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.9182
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-22
copyright: © 2020 Vollstedt et al.
attribution name: Vollstedt et al.

A game-theoretic model of Monkeypox to assess vaccination strategies
type: item
type: AcademicArticle
description: Monkeypox (MPX) is a zoonotic disease similar to smallpox. Its fatality rate is about 11% and it is endemic to the Central and West African countries. In this paper, we analyze a compartmental model of MPX dynamics. Our goal is to see whether MPX can be controlled and eradicated by voluntary vaccinations. We show that there are three equilibria—disease free, fully endemic and previously neglected semi-endemic (with disease existing only among humans). The existence of semi-endemic equilibrium has severe implications should the MPX virus mutate to increased viral fitness in humans. We find that MPX is controllable and can be eradicated in a semi-endemic equilibrium by vaccination. However, in a fully endemic equilibrium, MPX cannot be eradicated by vaccination alone.
format: application/pdf
format: text/html
creator: Sri Vibhaav Bankuru
creator: Samuel Kossol
creator: William Hou
creator: Parsa Mahmoudi
creator: Jan Rychtář
creator: Dewey Taylor
subject: Mathematical Biology
subject: Global Health
subject: Health Policy
subject: Infectious Diseases
description: doi:10.7717/peerj.9272
publisher: PeerJ Inc.
rights: © 2020 Bankuru et al.
abstract: Monkeypox (MPX) is a zoonotic disease similar to smallpox. Its fatality rate is about 11% and it is endemic to the Central and West African countries. In this paper, we analyze a compartmental model of MPX dynamics. Our goal is to see whether MPX can be controlled and eradicated by voluntary vaccinations. We show that there are three equilibria—disease free, fully endemic and previously neglected semi-endemic (with disease existing only among humans). The existence of semi-endemic equilibrium has severe implications should the MPX virus mutate to increased viral fitness in humans. We find that MPX is controllable and can be eradicated in a semi-endemic equilibrium by vaccination. However, in a fully endemic equilibrium, MPX cannot be eradicated by vaccination alone.
bibliographic citation: Bankuru et al. (2020) A game-theoretic model of Monkeypox to assess vaccination strategies. PeerJ 8:e9272 https://doi.org/10.7717/peerj.9272
date submitted: 2020-01-08
date accepted: 2020-05-11
issued: 2020-06-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bankuru
  given name: Sri Vibhaav
author list: Agent
  family name: Kossol
  given name: Samuel
author list: Agent
  family name: Hou
  given name: William
author list: Agent
  family name: Mahmoudi
  given name: Parsa
author list: Agent
  family name: Rychtář
  given name: Jan
author list: Agent
  family name: Taylor
  given name: Dewey
doi: 10.7717/peerj.9272
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-22
copyright: ©2020 Bankuru et al.
attribution name: Bankuru et al.

Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants
type: item
type: AcademicArticle
description: Background Glaesserella parasuis (G. parasuis) is a respiratory pathogen of swine and the etiological agent of Glässer’s disease. The structural organization of genetic information, antibiotic resistance genes, potential pathogenicity, and evolutionary relationships among global G. parasuis strains remain unclear. The aim of this study was to better understand patterns of genetic variation, antibiotic resistance factors, and virulence mechanisms of this pathogen. Methods The whole-genome sequence of a ST328 isolate from diseased swine in China was determined using Pacbio RS II and Illumina MiSeq platforms and compared with 54 isolates from China sequenced in this study and 39 strains from China and eigtht other countries sequenced by previously. Patterns of genetic variation, antibiotic resistance, and virulence mechanisms were investigated in relation to the phylogeny of the isolates. Electrotransformation experiments were performed to confirm the ability of pYL1—a plasmid observed in ST328—to confer antibiotic resistance. Results The ST328 genome contained a novel Tn6678 transposon harbouring a unique resistance determinant. It also contained a small broad-host-range plasmid pYL1 carrying aac(6’)-Ie-aph(2”)-Ia and blaROB-1; when transferred to Staphylococcus aureus RN4220 by electroporation, this plasmid was highly stable under kanamycin selection. Most (85.13–91.74%) of the genetic variation between G. parasuis isolates was observed in the accessory genomes. Phylogenetic analysis revealed two major subgroups distinguished by country of origin, serotype, and multilocus sequence type (MLST). Novel virulence factors (gigP, malQ, and gmhA) and drug resistance genes (norA, bacA, ksgA, and bcr) in G. parasuis were identified. Resistance determinants (sul2, aph(3”)-Ib, norA, bacA, ksgA, and bcr) were widespread across isolates, regardless of serovar, isolation source, or geographical location. Conclusions Our comparative genomic analysis of worldwide G. parasuis isolate…
format: application/pdf
format: text/html
creator: Xiulin Wan
creator: Xinhui Li
creator: Todd Osmundson
creator: Chunling Li
creator: He Yan
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.9293
publisher: PeerJ Inc.
rights: © 2020 Wan et al.
abstract: Background Glaesserella parasuis (G. parasuis) is a respiratory pathogen of swine and the etiological agent of Glässer’s disease. The structural organization of genetic information, antibiotic resistance genes, potential pathogenicity, and evolutionary relationships among global G. parasuis strains remain unclear. The aim of this study was to better understand patterns of genetic variation, antibiotic resistance factors, and virulence mechanisms of this pathogen. Methods The whole-genome sequence of a ST328 isolate from diseased swine in China was determined using Pacbio RS II and Illumina MiSeq platforms and compared with 54 isolates from China sequenced in this study and 39 strains from China and eigtht other countries sequenced by previously. Patterns of genetic variation, antibiotic resistance, and virulence mechanisms were investigated in relation to the phylogeny of the isolates. Electrotransformation experiments were performed to confirm the ability of pYL1—a plasmid observed in ST328—to confer antibiotic resistance. Results The ST328 genome contained a novel Tn6678 transposon harbouring a unique resistance determinant. It also contained a small broad-host-range plasmid pYL1 carrying aac(6’)-Ie-aph(2”)-Ia and blaROB-1; when transferred to Staphylococcus aureus RN4220 by electroporation, this plasmid was highly stable under kanamycin selection. Most (85.13–91.74%) of the genetic variation between G. parasuis isolates was observed in the accessory genomes. Phylogenetic analysis revealed two major subgroups distinguished by country of origin, serotype, and multilocus sequence type (MLST). Novel virulence factors (gigP, malQ, and gmhA) and drug resistance genes (norA, bacA, ksgA, and bcr) in G. parasuis were identified. Resistance determinants (sul2, aph(3”)-Ib, norA, bacA, ksgA, and bcr) were widespread across isolates, regardless of serovar, isolation source, or geographical location. Conclusions Our comparative genomic analysis of worldwide G. parasuis isolate…
bibliographic citation: Wan et al. (2020) Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants. PeerJ 8:e9293 https://doi.org/10.7717/peerj.9293
date submitted: 2019-12-24
date accepted: 2020-05-13
issued: 2020-06-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Xiulin
author list: Agent
  family name: Li
  given name: Xinhui
author list: Agent
  family name: Osmundson
  given name: Todd
author list: Agent
  family name: Li
  given name: Chunling
author list: Agent
  family name: Yan
  given name: He
doi: 10.7717/peerj.9293
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-22
copyright: ©2020 Wan et al.
attribution name: Wan et al.

A revision of the pelomedusoid turtle Jainemys pisdurensis from the Late Cretaceous (Maastrichtian) Lameta Formation of India
type: item
type: AcademicArticle
description: Background Jainemys pisdurensis comb. nov. is an extinct pleurodiran turtle from the Late Cretaceous (Maastrichtian) of India, previously referred to Carteremys and Shweboemys. The holotype, an eroded skull, had been collected near the village of Pisdura, south of Nagpur, in Maharashtra State, while all referred shell material originates from coeval sediments exposed at the nearby village of Dongargaon. Initial estimates believed this turtle to either be an early representative of Podocnemididae or a basal representative of Pelomedusoides. Methods We here figure and describe all specimens that had previously been referred to Jainemys pisdurensis comb. nov. We furthermore re-evaluate the validity of this fossil turtle and explore its phylogenetic relationships within Pleurodira. Results The holotype of Jainemys pisdurensis comb. nov. displays a morphology that differs substantially from that originally reported. Most notably, the palatines only have a minor contribution to the broad triturating surfaces but have a broad midline contact with each other, the pterygoids only have a midline contact of intermediate length and do not contact the opisthotics posteriorly, the basisphenoid is broad and short, and the opisthotics do not contribute to the flooring of the cavum acustico-jugulare. The referred shell material also displays a morphology different from that reported originally, in particular in that vertebral I does not contribute to the anterior margin of the carapace while the nuchal does. Phylogenetic analysis places the cranial material within the bothremydid clade Kurmademydini, while the shell material is placed in an unresolved polytomy at the base of this clade. Jainemys pisdurensis is confirmed to be a valid species of pleurodiran turtle, but the high diversity of coeval kurmademydines in India demands removal of the postcranial remains from this taxon. The realization that all valid species of Late Cretaceous (Maastrichtian) turtles from India form a clade…
format: application/pdf
format: text/html
creator: Walter G. Joyce
creator: Saswati Bandyopadhyay
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9330
publisher: PeerJ Inc.
rights: © 2020 Joyce and Bandyopadhyay
abstract: Background Jainemys pisdurensis comb. nov. is an extinct pleurodiran turtle from the Late Cretaceous (Maastrichtian) of India, previously referred to Carteremys and Shweboemys. The holotype, an eroded skull, had been collected near the village of Pisdura, south of Nagpur, in Maharashtra State, while all referred shell material originates from coeval sediments exposed at the nearby village of Dongargaon. Initial estimates believed this turtle to either be an early representative of Podocnemididae or a basal representative of Pelomedusoides. Methods We here figure and describe all specimens that had previously been referred to Jainemys pisdurensis comb. nov. We furthermore re-evaluate the validity of this fossil turtle and explore its phylogenetic relationships within Pleurodira. Results The holotype of Jainemys pisdurensis comb. nov. displays a morphology that differs substantially from that originally reported. Most notably, the palatines only have a minor contribution to the broad triturating surfaces but have a broad midline contact with each other, the pterygoids only have a midline contact of intermediate length and do not contact the opisthotics posteriorly, the basisphenoid is broad and short, and the opisthotics do not contribute to the flooring of the cavum acustico-jugulare. The referred shell material also displays a morphology different from that reported originally, in particular in that vertebral I does not contribute to the anterior margin of the carapace while the nuchal does. Phylogenetic analysis places the cranial material within the bothremydid clade Kurmademydini, while the shell material is placed in an unresolved polytomy at the base of this clade. Jainemys pisdurensis is confirmed to be a valid species of pleurodiran turtle, but the high diversity of coeval kurmademydines in India demands removal of the postcranial remains from this taxon. The realization that all valid species of Late Cretaceous (Maastrichtian) turtles from India form a clade…
bibliographic citation: Joyce et al. (2020) A revision of the pelomedusoid turtle Jainemys pisdurensis from the Late Cretaceous (Maastrichtian) Lameta Formation of India. PeerJ 8:e9330 https://doi.org/10.7717/peerj.9330
date submitted: 2020-04-06
date accepted: 2020-05-19
issued: 2020-06-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Joyce
  given name: Walter G.
author list: Agent
  family name: Bandyopadhyay
  given name: Saswati
doi: 10.7717/peerj.9330
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-22
copyright: © 2020 Joyce and Bandyopadhyay
attribution name: Joyce and Bandyopadhyay

Salticidae (Arachnida, Araneae) of Thailand: new species and records of Epeus Peckham & Peckham, 1886 and Ptocasius Simon, 1885
type: item
type: AcademicArticle
description: The study is based on new material from the collections of the Naturalis Biodiversity Centre in Leiden (RNHM) and the Hungarian Natural History Museum (HNHM) and addresses issues in two genera: Epeus Peckham & Peckham, 1886 and Ptocasius Simon, 1885 from Thailand. Both genera are of Asian/Indomalayan origin, the latter with a diversity hotspot in the subtropical valleys of the Himalayas. Based on morphological data, we propose three new species of Epeus (Epeus daiqini sp. nov. (♂♀), Epeus pallidus sp. nov. (♀), Epeus szirakii sp. nov. (♀)) and two new species of Ptacasius (Ptocasius metzneri sp. nov. (♂♀) and Ptocasius sakaerat sp. nov. (♀)). Additionally, we redescribed E. tener (Simon, 1877) and added photographs of morphological characters. The genus Ptocasius is redefined due to the inclusion of 37 species, previously included in Yaginumaella Prószyński, 1979. Relationships and distribution of both genera are discussed in reference to molecular, morphological and distributional data, published by other authors in recent years.
format: application/pdf
format: text/html
creator: Barbara Maria Patoleta
creator: Joanna Gardzińska
creator: Marek Żabka
subject: Biodiversity
subject: Biogeography
subject: Entomology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9352
publisher: PeerJ Inc.
rights: © 2020 Patoleta et al.
abstract: The study is based on new material from the collections of the Naturalis Biodiversity Centre in Leiden (RNHM) and the Hungarian Natural History Museum (HNHM) and addresses issues in two genera: Epeus Peckham & Peckham, 1886 and Ptocasius Simon, 1885 from Thailand. Both genera are of Asian/Indomalayan origin, the latter with a diversity hotspot in the subtropical valleys of the Himalayas. Based on morphological data, we propose three new species of Epeus (Epeus daiqini sp. nov. (♂♀), Epeus pallidus sp. nov. (♀), Epeus szirakii sp. nov. (♀)) and two new species of Ptacasius (Ptocasius metzneri sp. nov. (♂♀) and Ptocasius sakaerat sp. nov. (♀)). Additionally, we redescribed E. tener (Simon, 1877) and added photographs of morphological characters. The genus Ptocasius is redefined due to the inclusion of 37 species, previously included in Yaginumaella Prószyński, 1979. Relationships and distribution of both genera are discussed in reference to molecular, morphological and distributional data, published by other authors in recent years.
bibliographic citation: Patoleta et al. (2020) Salticidae (Arachnida, Araneae) of Thailand: new species and records of Epeus Peckham & Peckham, 1886 and Ptocasius Simon, 1885. PeerJ 8:e9352 https://doi.org/10.7717/peerj.9352
date submitted: 2020-01-28
date accepted: 2020-05-23
issued: 2020-06-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Patoleta
  given name: Barbara Maria
author list: Agent
  family name: Gardzińska
  given name: Joanna
author list: Agent
  family name: Żabka
  given name: Marek
doi: 10.7717/peerj.9352
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-22
copyright: ©2020 Patoleta et al.
attribution name: Patoleta et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359